i've actually had this happen, but im not saying its what you've got happening as well.

over the last few days ive been really tired and end up with 2 of the keyclones loaded, which means anything that gets broadcasted means it will be added to the windows twice.

i also found on some occasions that it double added windows due to me messing around, so be sure to check that only the windows you want are listed inside keyclone.

this may not be of any help, but it does happen that people miss the obvious sometimes.