Well, no not really. Unless for some really weird reason I'd rather not think about SPWAW somehow leaves something in memory that turns off SE4's animation of ship movement. Can be done from system menu. Do you have that on or off normally? Doesn't explain the faster loadtimes though.
Maybe SPWAW has some built in performance enhancer that stays active after the game is shut down?
I don't know, but be thankfull.
