Is Keyclone loading your instances of wow? If so then it's the maximizer settings that determine the size of the regions and what resolution those regions are rendered at. Make sure that the commands loading the different instances of WoW are putting them in the right regions. What I just found out today is that you need to make the WoW settings be windowed, Keyclone does not seem to pass the windowed flag to the wow.exe. Also make sure your keyclone has the right permissions to save its settings or it wont accept any of your tweak changes and they will be gone next run... Thats all I can think of to check.

If you look at Step 5 of the Software Setup on this page you see it walk through setting up Maximizer as a large part of it.