i thought it was jus me but:
Rarely, enemy ships won't be affected by my weapons. My weapons hit sheilds, i can collide with them, hit them with missiles, but my primaries pass right through them. After forcing myself to collide with an enemy ship the problem usually goes away, then it might come back, then go away, and eventually it stays away after a few minutes.
It doesn't happen very often, i think i remember it happening in the main freespace 2 campaign as well as user campaigns.
I posted this on the hard light forum but now that i know it's not just me maybe it's something you guys could look into, thanks.