Does the problem happen with a different video card? Or with a different monitor?
I observed this problem with MSI Radeon HD 4670 card.
Then I tried older Nvidia GeForce 9600 GT card and also Radeon HD 5450 card.
The problem seems to go away with the other two cards.
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In that case, I would be led to believe that the problem is being caused by a compatibility conflict. For troubleshooting, I can recommend running the latest BIOS version, and updating the firmware on the card itself.
I'm using the latest BIOS (May 16, 2011).
The same graphics card works just fine in another MSI X58 Pro based system, so I'm sure there is some problem in this specific combination.
Anyway, the card was cheap so I just decided to get another newer card (AMD Radeon 5450) which works fine with dual monitors.
I'm glad to hear that you were able to solve the problem. We'll forward your information to our development department.