I'm having the same issue.. Set up the double VGA properly but the wow windows are "not syncronized" as confusedtx5 has explained..

This is my setup..
Primary adapter --> Ati Radeon 4780 1GB connected to Monitor 1
Second adapter --> Ati Radeon 4780 1GB connected to Monitor 2

Primary video - Main Character Maestrale
Secondary video - 4 alts

When i enable the mouse/keyboard repeater, i see the "fake" mouse cursor on the 4 alts, but when i move the mouse...
sorry for my english, i'm not able to explain... look at the picture below.. is better explaining
The GOLD trace is the mouse movement - repeated bad on the alts windows.



Both monitors are 22", same resolution 1680*1050, game profile of the 5 pg in game are the same for all pg on all screen/ wow istance (1680*1050)
BUT
In the secondary monitor the single "alt" window looks like is not set properly to 1680*1050 but lowered to a kind of 800*600 ----- so the mouse movement on different resolution windows is different!

Hope there will be a solution that is NOT to set Main pg resolution to 800*600 or something... this will be really bad..