If you can set one BOFF... Put them into a station. Click the same station, and assign another to it.
The 'new BOFF will show up. Click your next station, and assign your first boff (the one you were able to assign). Repeat the procedure until every slot is filled... (I found this out by accident, but, it works)
Having this problem too with the blockade runner. I can assign 4/5 of my officers. Yes all the boffs are of appropriate type. i've even dismissed a bugged officer. When i picked up a new one I could put him in, but then it popped a different one out and I can't get him back in.