I have that problem in the TGEIII game. I have noticed it's more noticable when I do turns on my laptop then on my desktop. There's still a lag on the desktop, but it's tolerable. It's probably a function of how beefed up your pc is with the memory and the processor. Which would explain why a techo-crat like SJ hasn't noticed the problem.
And SJ's suggestion about retrofitting in small batches does work. That's what I do on my laptop. Only problem is you have to watch carefully which ships you are retrofitting. You are supposed to stay in the current position in the list, but sometimes it jumps around. And if you lose your place there is no convienent way to know which ships you've already given the retrofit order to.