This code works
WeaponSet
Conditions = None
; -----
Weapon = PRIMARY HammerheadRailgun
PreferredAgainst = PRIMARY VEHICLE STRUCTURE
AutoChooseSources = PRIMARY FROM_PLAYER FROM_SCRIPT FROM_AI
; -----
Weapon = SECONDARY BurstCannon
PreferredAgainst = SECONDARY INFANTRY
AutoChooseSources = SECONDARY FROM_PLAYER FROM_SCRIPT FROM_AI
End
I think your problem is that you have two weapons set to the same "PreferredAgainst=" type.....thing.