Obviously a bug fix is needed for all of the errors. The concept of this software is fantastic, but execution is a little off. Take some time to go through the bugs.
Second, I think if the program allowed multiple desktop environments, such as Ubuntu does (you can click a box to switch to another desktop area, where there are no windows from the other desktop. It's a virtual solution to the entire 'Too many windows to manage' problem. Plus, it would allow the end user to organize their windows even better.