I've been finding the way the new Mac Pro deals with multiple outputs through the mini display ports increasingly temperamental, especially using different resolutions. Having to work through active and passive Dvi connections. The best fix I've gone through is to send them all through a matrix unit and switch them accordingly if issues arise.
I've found using SwitchresX can be helpful too, having the software to open on startup and set to go to the last saved settings for the connected outputs.
It''s all very much work in progress still though, to get some consistency an piece of mind.