Well I just looked at the CGSovereign and I have found the problem: Some Hardpointers to have a strange point of view: the Quantum Launchers of this ships doesn't have a recharge rate: Now when you set your weapon Power to 0 with APM enabled the Launchers will all be unloaded - I found that much more logical as the old games way. Now when you restore power to them, the turrets doesn't recharge because their recharge rate of 0. For a simple work-around for this problem: Open the Hardpoint file of the CGSovereign, Search for SetRechargeRate(0) and replace it with its cooldown value. For the CGSovereign the cooldown value is 10, so use instead SetRechargeRate(10)
Excellent, I'll give that a try.
Unfortunatly that will mean your torpedo load 'recharges', while its not realistic, it does get round the problem.