The "Default" versions are more like the "base" version that everything else is built from. The "XCom" versions in the My Games folder are the versions that are built/updated when the game launches. These are built by merging the "Default" version with any "XCom" versions of mod files in DLC or mods (functionally, DLC and mods integrate into the game in the same way). One very important thing to realize is that the versions in the My Games folder are rebuilt using file timestamp information. So, if a mod applies a delta file that removes/changes a line that was in the Default, if the mod is made inactive or even deleted, the versions in the My Games won't be updated (because timestamps haven't been changed). This will result in inactive/delete mods "leaking" into cases where they shouldn't. Firaxis is aware of this issue. The current workaround is to delete the config files in the My Games folder to force the game to rebuild them. This will be necessary when removing or not using a mod that makes adjustements to the Default configurations. This is actually a common problem in Unreal Engine 3, and was something that often had to be done with Long War for EU and EW. Thanks Amineri, this was precisely my issue.