Happened to me recently in the all-mod file. It got corrupted and now I am doing it again from scratch (re-testing all the way, 2 days now half way done). I've decided NOT to include EVERYTHING like I did before but only the best and most unique stuff. I mean 10 types of cyclops where the only difference is the name is silly. but one like the Excaliber with a unique .pof at least sets it apart... I will end up enabling some basic FS2 weapons for the mod player ships like the Subach-7 and Rockeye/ Tempest.Hornet, and Trebuchet. That way no matter what you fly (Angel to X-Wing) you can use a basic weapon and it won't make FS2 work so hard in the weaps table. Less new weaps means less chance for conflicts... I really went nutz last time and learned my lesson (sorta)
here's 2 pics of the Weapons from Tales of the EA Janus (A Bab5 mod campaign) they are the Nova-X front Beam and The Narn Laser... I couldn't get the Nova

Laser to work just the Front ones in the

slots. These weapons are in the VP file of that mod campaign. Also the Shadow skinned Nova-X destroyer is there BUT though it works in game it will NOT fire weapons (Beam free no effect) it has turrents and pof data seems fine)... Mounted the new weapons on a regualr Nova and they worked!!! Screens:
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