Did you remove all earlier versions of mods in your mod folder? You should never overwrite mods. First delete the old versions before extracting the new ones.
Or is the game laggy? Might be a memory issue. Try disabling one or two mods, like Project Valkyrie or Kadur Theocracy.
Other than that, I don't know what the issue could be.
Yes, I did remove all previous mods...
Nope, it's not laggy...
Okay, I'll try to disable a few mods...
Maybe this will help you to figure out what's the problem, it's from starfarer log...
217403 [Thread-6] ERROR com.fs.starfarer.combat.D - java.lang.OutOfMemoryError
java.lang.OutOfMemoryError
at sun.misc.Unsafe.allocateMemory(Native Method)
at java.nio.DirectByteBuffer.<init>(DirectByteBuffer.java:99)
at java.nio.ByteBuffer.allocateDirect(ByteBuffer.java:288)
at org.lwjgl.BufferUtils.createByteBuffer(BufferUtils.java:60)
at com.fs.graphics.TextureLoader.o00000(Unknown Source)
at com.fs.graphics.TextureLoader.o00000(Unknown Source)
at com.fs.graphics.TextureLoader.o00000(Unknown Source)
at com.fs.starfarer.util.ReplaceableSprite.?0O000(Unknown Source)
at com.fs.starfarer.campaign.BackgroundAndStars.super.super(Unknown Source)
at com.fs.starfarer.campaign.BaseLocation.renderBG(Unknown Source)
at com.fs.starfarer.campaign.CampaignEngine.renderBG(Unknown Source)
at com.fs.starfarer.campaign.A.รด?0000(Unknown Source)
at com.fs.starfarer.new.???000(Unknown Source)
at com.fs.oOOO.super.new(Unknown Source)
at com.fs.starfarer.combat.D.o00000(Unknown Source)
at com.fs.starfarer.StarfarerLauncher$2.run(Unknown Source)
at java.lang.Thread.run(Thread.java:619)