I tried moving Starsector to my desktop and running the debug, then again as admin, to no avail. Though the error log did look slightly different. Also by run configuration I assume you mean the config I have on IDEA for running the bat file? I'm still very new to all this. Regardless, I will post a screenshot of that. If anything else is needed, let me know. It helps to be specific.
Your debug-starsector.bat is not specifying java.library.path. It should look like this (since you are on Windows, you can just copy/paste the entire thing):
start ..\jre\bin\java.exe -agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=5005 -Djava.library.path=native\windows -Xms1536m -Xmx1536m -Xss2048k -Dcom.fs.starfarer.settings.paths.logs=. -Dcom.fs.starfarer.settings.paths.saves=../saves -Dcom.fs.starfarer.settings.paths.screenshots=../screenshots -Dcom.fs.starfarer.settings.paths.mods=../mods -classpath janino.jar;commons-compiler.jar;commons-compiler-jdk.jar;starfarer.res.jar;starfarer.api.jar;starfarer_obf.jar;jogg-0.0.7.jar;jorbis-0.0.15.jar;json.jar;lwjgl.jar;lwjgl_util_applet.jar;jinput.jar;lwjgl_test.jar;log4j-1.2.9.jar;lwjgl_util.jar;fs.sound_obf.jar;fs.common_obf.jar;xstream-1.4.10.jar com.fs.starfarer.StarfarerLauncher
The following option is of particular relevance:
-Djava.library.path=native\windows
You should also set up a run configuration for attaching a debugger to Starsector. To do this, click + on the top-left of "Run/Debug Configurations" and select "Remote JVM Debug". Use the following settings:
Debugger mode: Attach to remote JVM
Transport: Socket
Host: localhost
Port: 5005
Command line arguments for remote JVM: -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=5005
Use module classpath: <your mod>
Before launch: Run another configuration -> run the debug-starsector batch script.