Happens here as well...
I have a different setup and always used 2 DL monitors -- Syncmaster 940UX -- with a Mac mini (10.6). Often when I upgrade the beta, most recently with 1.6 beta 2, this happens.
BUT, different then your situation, it eventiually stops happening, and stays okay ... until the next upgrade.
I have no idea what I do that corrects the problem, just keep moving things around in Preferences/Displays until, on the next boot, it's okay.
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