the lobby update about the mod vault broke UI mods for many players (they wouldn't show up in the FAF mod mananger, and be disabled on game launch), here is how to fix them:
1) locate the install location of Supcom FA, enter the \mods folder and copy paste all broken mods
2) go to C:\Users\<YourUsername>\Documents\My Games\Gas Powered Games\Supreme Commander Forged Alliance\Mods and paste them there
3) if you got a mod in a .zip version (example hotbuild): create a similar named folder, drag it into, extract it there and then delete the now obsolete .zip file
4) enter the mod vault in FAF, and enable all your UI mods (white coloured), they should show up now
5) host a game, enable them in the FA lobby again
6) have fun
(did this myself, it did not force me to reset the keymap for hotbuild, all the usual settings still worked)