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So every so often a cmd.exe like window would flash for a moment and then disappear. But I'm never able to see exactly what it did. Any way I can find out?

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I would suggest you check your PC for malware first. Probably you can figure out what's causing this via something like Process Monitor, after filtering out only events related to the cmd.exe process. – Karan Oct 21 '12 at 22:37
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You could use the Process Monitor to log the activity in your system

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