I'm not sure exactly if this is indeed as it should or shouldn't be, or if you're even aware of this fact. I was browsing though the FS General forum in a thread discussing which events in which missions give the player access to new ships and weapons. I noticed that one in "The Great Hunt" gives the player access to the Cyclops#short, not the Cyclops as you would expect. I'm not sure if this is how its supposed to be, but it may be an indication of where the problem lies. Now, I took a look for myself, by extracting the mission and looking through it in FRED2 (not Open for authenticity purposes) and confirmed the event for myself. Since you haven't made your own somewhat altered version of this mission (a la "Slaying Ravana", still not sure what you changed though... anyway) the only conclusion I can come to (assumint this IS the problem) is that in your merged FS1-FS2 weapons.tbl file, the #short is somehow being swapped for the standard Cyclops in this event, creating the problem that affects the weapon thoughout the entire campaign. Once I finish my current player, I will try to alter this mission to change the event to the Cyclops, and see if this makes any difference... unless, of course, someone else does this first... hint, hint.