Without "hopefully" getting into too much detail. If you're using the Keyclone maximizer option, then you want to make sure that each of the command lines (wow1, wow2, etc) match up with the REGION number in the maximizer section of Keyclone. If they don't, or you start a WoW instance without a region, it defaults to full screen.

Sounds like that's the issue you're having. Hope this helps.