Okay, now that's interesting... Which version of Mantle are you running? Maybe Kestrellius did actually change something in updates? Also, maybe using a different build (i.e. 3.8.0-3 vs latest nightlies) changes something?
Eventually, you can toggle your and only your own primaries and secondaries with cheats, if you want. It might be just to "help yourself" pass a mission and then the next one will have more sensible loadouts?