I have been searching for the past 2 hours trying to fix this error message when I save. It is not the dual monitors and there is nothing hiding beneath the three main windows. Can anyone please help? Thanks.

This is worth a try. Goto...

View > Open Windows > Close All

Something is bugged out if that doesnt work. If you continue to have this problem you can also try the allow unsafe save in the creationkit ini file. This ini is only applied on startup so it wont help you this time.