I tried your new build Alex and it unfortunately doesn't fix the problem. The problem being exactly what Dark Revenant described.
Edit: Here's my log.
0 [main] INFO com.fs.starfarer.StarfarerLauncher - Starting Starsector 0.8.1a-dev2 launcher
1 [main] INFO com.fs.starfarer.StarfarerLauncher - Running in C:\Games\Starsector2\starsector-core
2 [main] INFO com.fs.starfarer.StarfarerLauncher - OS: Windows 8.1 6.3
2 [main] INFO com.fs.starfarer.StarfarerLauncher - Java version: 1.7.0_79 (64-bit)
23 [main] INFO com.fs.starfarer.settings.StarfarerSettings - Loading settings
26 [main] INFO com.fs.starfarer.loading.LoadingUtils - Loading JSON from [ABSOLUTE_AND_CWD: null (data/config/settings.json)]
22292 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 640x480, 144Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 640x480, 60Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 640x480, 59Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 640x480, 75Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 640x480, 67Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 640x480, 85Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 640x480, 100Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 640x480, 120Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x480, 144Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x480, 85Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x480, 72Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x480, 75Hz, 32bpp
22294 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x480, 120Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x480, 100Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x480, 56Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x480, 60Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x576, 72Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x576, 75Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x576, 85Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x576, 100Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x576, 120Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x576, 60Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x576, 56Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 720x576, 144Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 800x600, 144Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 800x600, 56Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 800x600, 60Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 800x600, 120Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 800x600, 100Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 800x600, 85Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 800x600, 72Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 800x600, 75Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1024x768, 144Hz, 32bpp
22295 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1024x768, 60Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1024x768, 100Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1024x768, 120Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1024x768, 70Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1024x768, 75Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1024x768, 85Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1152x864, 75Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1152x864, 85Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1152x864, 100Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1152x864, 120Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1152x864, 60Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1152x864, 144Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x720, 120Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x720, 100Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x720, 85Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x720, 60Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x720, 59Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x720, 50Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x1024, 144Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x1024, 75Hz, 32bpp
22296 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x1024, 85Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x1024, 100Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x1024, 120Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x720, 144Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x1024, 60Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x960, 120Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x800, 144Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x960, 100Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x768, 144Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x960, 85Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x960, 60Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x768, 60Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x800, 60Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x800, 85Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x768, 120Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x768, 100Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x768, 85Hz, 32bpp
22297 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x960, 144Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x800, 120Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1280x800, 100Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x1024, 144Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x1024, 60Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x1024, 85Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x1024, 120Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x1024, 100Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x768, 144Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x768, 100Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x768, 120Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x768, 85Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1360x768, 60Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1366x768, 144Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1366x768, 100Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1366x768, 120Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1366x768, 85Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1366x768, 60Hz, 32bpp
22298 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1440x900, 144Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1440x900, 60Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1440x900, 85Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1440x900, 120Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1440x900, 100Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1600x900, 85Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1600x900, 100Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1600x900, 120Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1600x900, 60Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1600x900, 144Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1680x1050, 120Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1680x1050, 100Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1680x1050, 85Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1680x1050, 60Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1680x1050, 144Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1920x1080, 85Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1920x1080, 120Hz, 32bpp
22299 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1920x1080, 100Hz, 32bpp
22300 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1920x1080, 59Hz, 32bpp
22300 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1920x1080, 60Hz, 32bpp
22300 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1920x1080, 50Hz, 32bpp
22300 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Found display mode: 1920x1080, 144Hz, 32bpp
22300 [main] INFO com.fs.starfarer.launcher.opengl.GLLauncher - Assuming native monitor resolution is 1920x1080
47486 [Thread-2] INFO com.fs.graphics.OO0O - Using refresh rate:144
47884 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/ui/launcher_bg.jpg (using cast)
47913 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/ui/launch_button_bg.png (using cast)
47917 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/ui/play_button0.png (using cast)
47920 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/ui/play_button1.png (using cast)
47923 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/ui/buttons/toggleA20x_on.png (using cast)
47925 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/ui/buttons/toggleA20x_off.png (using cast)
47927 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/ui/buttons/arrow_down.png (using cast)
47929 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/fx/scanline11.png (using cast)
47944 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/fonts/orbitron24aabold_0.png (using cast)
47963 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/fonts/orbitron20aa_0.png (using cast)
47977 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/fonts/insignia15LTaa_0.png (using cast)
47987 [Thread-2] INFO com.fs.graphics.TextureLoader - Cleaned buffer for texture graphics/fonts/orbitron12_0.png (using cast)