its because of the way the pulse weapons were set, the CG soveriegn will do this too. Because he was trying to mimic a quantum torpedo launcher, the tube has a finite charge and a recharge rate of zero, so the pulse weapon will eventually run out of shots. Unfortunately, since the tube shuts down when you stand down from red alert, it will not recharge when you activate it again, because it lost whatever charge it had left when you stood down. The only way to fix this is to change the recharge rate on all the turrets in the hardpoint file.