I seem to recall a problem with the change from 9 to 10 or 10 to 11 whereby the surfaces of the window frame and sash were deemed to be touching, and therefore cleaned up without a line between. Try changing the sash (inner frame) material to something different to the main frame material. You could make a copy of main frame material with a different name, that would do.
See if that works. Still a pain if you have to do this with all your windows, but you should be able to select them all and change the one parameter o.k.