I remember getting a strange problem a while ago where I could only get a certain number of ships to show up in the loadout screen (e.g. if I selected all the ships in a mission, it only went up to the Artemis DH and did not show anything under that), but that was only in the game and the limit was high enough as to not really that much of an issue in practice. My tables were wiped out at one point though and I had to rewrite everything, at which point it ceased to become a problem, so there must have been something wrong in there.
I don't think it has anything to do with the weapon bank specifications, since I once even had weapons in there that did not exist in the game, but it just ignored the bad entries and worked fine.
It might possibly be related to the ordering of the entries in the table file, though.