Please see the most recent updates in the "Where did the .com name go?" thread. Posts number 16 and 17.
I've seen this before too. You may have to manually "shut down" the offending panel. For example, if the Captain's panel is Shift+1, and the FO is Shift+2, you may have to go Shift+1 then Shift+2 to go from the Captain's view to the FO's for example.
I hope this helps ....
Daniel
Tommy - I think that is the way they made the panel.cfg apply the windows. You need to "undo" each one to avoid the overlaps . .