I, too, have been having this problem. I'm also running on a Vortexbox appliance, with Custom Scan and Custom Browse enabled. It stopped happening for several weeks, and then started up again a few weeks ago. The couple of times that I've managed to log in while the problem was happening, mysql was sucking up most of the CPU. When exactly is mysql supposed to be active? Only during a scan? Unless I'm missing something, I don't think I have any automatic scanning enabled.
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