I have the same problem. On my system it's caused by the WoW windows not losing focus after using PiP. Try this:

(assuming maxfpsbk=10 and maxfps=50)
1. Turn on FPS display in all your copies of WoW (ctrl-R by default).
2. Verify that the unfocused ones are at your maxfpsbk cap of 10 and that the main window is at 50 (or whatever your settings are).
3. In your main window cycle through all your PiP windows using hotkeys, pausing for 4-5 seconds between swaps and without moving your mouse out of the main window.
4. Observe the FPS in all windows - the expected result is that all slave windows would be at 10 fps - but on my system all slave windows and the main window are at 50 fps.

The workaround (if your problem is the same as mine) is to move your mouse into the slave window for a second then move the mouse out - then the window will truly lose focus and the fps will drop back to 10 (assuming you use some form of focus follows mouse).

If you're interested keyclone I'm running on win xp pro 64 bit with a 7800gt video card and 4gb ram. Clean installed system, nothing extra. I'm using windows focus folllows mouse featyre - not the keyclone one.