Ok, These are all just shots in the dark.. but I dont like seeing No feedback to try and help out a fellow boxer.

How are your folders set up? Just one that they all run off of, hard copies of WoW or System link copies of wow? I ask cause I have not seen a fast speed 1TB drive so if its 5 separate folders I am wondering if its hard drive delay causing instabilities.

You can try cycling through the windows but I -highly- suggest doing 100% nothing while Keyclone launches all of your WoWs. I have had issues with trying to manipulate windows while they were loading, that actualy put me into the state ya describe below just with out the crashing (All of the screens thought they were the main screen so they were all chugging at like 45fps (Was capped at 60/15))

How are your graphical settings? Even on my system I turned everything down to minimal (Makes the nice sparklies hard to see some times for quest items but I am getting used to it). Could just be the initial load of the graphics that are poo.

Since you can see the frame rates I am assuming this happens In-Game and not at the loading menu or are you using something like FRAPs to give you a constant FPS display?

Thats all I can think off of the top of my head to ask or suggest.