Hi emgee and welcome to the forums!

check your keyclone list... odds are you have more then the 2 wows you want.
go to keyclone/setup/general and UNCHECK the auto-add... or CHECK the exact windows titled

what is probably happening is that keyclone is finding a window, probably windows explorer, with 'world of warcraft' in the titlebar... and automatically adds it to the keyclone list.

these days, i recommend dropping the auto-add and using commands to start your wows (along with maximizer)

check this link for a step-by-step guide on using commands and maximizer:
[Keyclone] setting up a command to work with maximizer (step-by-step)

if you have more questions, please feel free to drop me a note.

have a great night!