Nothing in GSX could possibly cause this, since in P3D, each addon has its own add-on.xml file, so they won't affect each other. GSX doesn't change anything in the Prepar3d.cfg file either, and the only change it does ( addint itself to the addon.cfg file ), it doesn't do it directly, but it ask the simulator itself to do it.
Do you use a 3rd party add-on.xml manager ?