Adam, can you reproduce this problem?
Maybe there is a solution by changing the use of classes or ID's for div tags? I am not sure how the fit-screen feature works since I'm new to CuteEditor. But I have still not managed to solve the issue - and I have been working with this far too many hours now, so I beg anyone who knows anything about this to reply.
I have updated the example here: http://www.aibility.com/test/
You can try the fit-to window button, then click the lnk to see an editor that actually maximizes on the same html/css base code.