VWEAP.x is the model that the enemies use (and drop). The pick-up is an entity, which is why it's showing up correctly. It sounds like you haven't overwritten the original template weapon's VWEAP file. It needs a single FIRESPOT bone for the muzzle flash. As for positioning, the weapon's centre of mass is attached to a bone in the character's hand, so it's really a matter of trial-and-error to get it in the right place. Also, this bone doesn't seem to be in exactly the same place in each character (I lined my FN P90 model up using the Model Pack 1 Specialist character, but in Aiko's hands it looks a bit off) so if the weapon is specific to a certain character, I'd use them for testing.
Hope this helps
- Graham