You sure this isn't related to the old "oh, I'm not in command anymore" bug, which however should only happen in select missions. Basically, when you order them to e.g. return to formation, will your guy say something like "All, follow 2!" instead of "Return to formation!"? In that case, just tell them you're 'done' (umm, can't remember the exact numbers, but it's basically in the "reply" menu I think, where stuff like "injured" and such are as well) and you should get your command back.
That's the only thing I can think of. Otherwise, corrupted installation, reinstall?
Wolfrug out.