RedAndCosmoteer
I don't know what to say, I think you have all the mods.
Although, if you're using Drak's updated Meranera's mods, make sure you have both Legacy AND Additional weapons on. Some ships use both types.
Other than that, maybe there was a slight oversight you had with one of the mods? Like you forgot to enable one of them, or they aren't updated to the latest version?