I've had a couple of odd things happen with WPMU DEV Dashboard and GD Press Tools.
With the WPMU DEV Dashboard the central content areas in all except the "support" option completely disappeared. It turned out that the central panel content was being pushed down below the bottom of the screen ~ which was why it seemed to have disappeared.
And GD Press Tools has issues too from time to time when sections of the menu system go white.
Should everything work with MP6 or is there some way to figure out what's compatible and what isn't? Or is this an issue that will be addressed in time?