That's just not how the GC3 system works... its reading every file in the Mod Folder... if a single file is misplaced, that single part will not work... there is no "this mod loaded" and "this mod didn't" its never a all or nothing affair unless you completely missed installing the mod properly.
If its not working, your likely getting an error message... whats the message?
And always double check that "Enable Mods" is checked in the options of GC3.