I've seen something similar in FS1, and here's the conclusion I came to.
I set up two Orions to fight each other, but one to have the Shivan Super Laser (rebel faction using Shivan tech). Well when I started the mission, BOTH Orions shot at each other with Super Lasers... and from the same turrets I gave to the rebel Orion.
What I figured is that when you assign special weapons to a ship, the game applies that same turret info to all ships of that class. I don't know why, but that's the conclusion I came to.
My solution: create two entries in the ships.tbl. One for each of the different turret configs.
Joe.
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www.joek.comRevelations: A FS2 Campaign