I used all three, protect, ignore and no dynamic goals. Actually now I think about it, I only checked no dynamic goals in the wings editor, not for individual ships.
I can't really say if ai.tbl has anything to do with it. One, I've never messed with it, and two, I tested it on a basic scp install (mediavps only). I suppose some errant table might mess things up though, it has certainly happened before. If I had to make a guess, I'd be more likely to pin the blame on species.tbl, that has caused all sorts of weird errors regardling AI behaviour. But you can just try the mission I put up and see for yourself - I know it works on the
build, so if it doesn't for you, it's something else.
But I'm not much of a modder so table problems honestly are really not my ballgame. I just FRED and occasionally try to get acquainted with the source. Well, mostly just the sexp part of it for now, since that seems the easiest point of entry.
Regardless, good luck

It sucks spending hours on a mission only to have something not work and not being able to find out why.