I can bet in your case it's not the disk I/O actually, unless you have some very strange emulator the file access should still go through the OS disk cache. VMware for example surely benefits from it. How many GB do you have on the machine? How much is still left free when you run the emulator and the other software you need?
I noticed it as disk i/o because I would leave task manager running on second screen and every time the game lagged memory and CPU use were below 30% and disk was 100%, and if I left sorting by disk usage, the first places are the windows stuff, and after them, the emulator.
