Well I think I pretty much fixed it. I changed a couple of things all at once, so I'm not sure what the real problem was.

I tured off Windows Aero, turned off V-Sync on all boxes, set my mains video settings from high to medium, zoomed in the view on clones, and used a pre-made maximizer setup.

This has made my main stay at a capped out 45fps (sometimes dropping to 40-44), and made swtiching between boxes using PiP almost instantaneous.

I still don't think I should be dropping fps at all with this setup, but for the time being this is a big improvement.

Edit: Kaynin, you said "Running four seperate dirs from one drive will put a lot of strain on your HD and is I think the most likely cause of your problems." Would buying an external HD serve as a good solution to this problem, or should I buy another HD for my computer, and get someone install it? Also, would size matter in this case, or is there any particular brand you reccomend (cost effective balanced with quality, please)?