Someone do me a favor. Put together a quick scrap mission that doesnt serve a purpose except to prove a point. Put two fenrises facing a lilith in the mission, then beam-free-all. Now, change the forward beam cannon on one of the fenrii to something like a BFRed. Just so you know it's different. Leave the other fenris alone. Save, and start FS2. Launch the mission and see what happens.
Incase you don't notice, both fenrii have BFReds, even though you only changed one of them. Now normally, you wouldnt do much of this. However, if you decide to make a campaign involving live-action R&D of new types of weapons, etc, it would bring in some problems.
Anyway, I'm surprised this hasn't been fixed yet. And I would assume it wouldn't be too hard to get a fix for it. And that's all I have to say about it.
BTW WMC, Get yer butt in IRC, I'm going to help you debug that modular bug of yours. I dont know how to write C++, but I can definately read it, and there looks to be some bad grammar in weapons.cpp, but then again, I could be wrong.