Have the exact same issue here. No injuries, but no matter who I put on the repair team and no matter what their rank or skill, the deck gun(s) and AA guns stay damaged until I can hit "Refit." Occasionally, though, the guns still operate even though they are "damaged." This is all a complete mystery to me, so perhaps I am insane as well.
@leovampire - what's the secret to getting the repairs made?