I second milbo's experience. PT7.4.2 mbox proII, rear FW on 2.8 8-core, 10GB RAM., DVToolkit 2. Exact problem and sometimes low CPU error (yeah, right) and toggling the clock source fixes it. You'll get an error after selecting SPDIF; just blow right by it. It won't matter since you're changing it back to internal anyway.
Prior to finding this work-around, I had been running the terminal script in the support tools folder, deleting preferences and databases. This worked, too, but it's a pain to reset all my preferences.
It's interesting that this same technique also fixed the intermittent white-noise problem with the first MBox back before Digi released the firmware update. Something about that clock...
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