I also am using 1.8k and Vista 64-bit, latest updates(sp1). I have the exact same problem, any alt I switch with my main never gets "demoted" and retains a high fps. This only happens with my main, if I switch from an Alt to another Alt, things work as expected. This issue is very annoying as I need to always click on the window after I swap my main out.

EDIT: I should also add, I am using a 9800gx2 with just one display. I have 1 main window that covers most of my screen with the 4 alts running on the right side, all using the exact same aspect ratio. PiP is very fast, even in places like orgrimmar. Also, I wonder if maybe having a macro fire while pressing the PiP key might be interfering? Ie. F12 is PiP and also is /focus Alt2