I don't think this problem has anything to do with the size of the database(s). It looks similar to
http://www.kinook.com/Forum/showthre...threadid=2344, so changing 'Tools | Options | General | Windows taskbar entries' to 'Always one for each open database' might work better for now.
I was not able to reproduce the problem with the files you sent, so we'll probably need to create a debugging build for you to run to help isolate the problem.