I have done that for all of them and created the pbo with Binpbo, and its still doing the same thing.

I am having the exact same issue. I have a Blufor, Indfor, and Civ faction that all load independently, but do not all load when together. I have tried them all in the same folder and all in different @mod/addons folders. It seems whichever one the game encounters first when loading is the one that gets loaded. I haven't tested that extensively, but it seems to be the case when trying different things. I can pm you the factions if necessary.