Ugh, I hope not. Playing with the sugar boats on full realism is an interesting challenge, but I'm sure the recharge rate, while possibly slower than the newer subs, was nowhere near as slow as that.
Anyway original problem solved;
Turns out the problem was a setting in the Nvidia control panel, antialiasing transparency was set to multisample somehow. That also affected another sim I play, Trainz train simulator, which was taking a longer time to focus textures - I was getting blurred textures in that game for 15-20 seconds after changing camera views.