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When I put the computer into sleep (manually, going from start menu, or when it automatically does it), the computer actually shuts down. Then, by itself, it starts up again, and gives me the "improper shutdown" error. I start Windows normally and it runs fine.

I removed the reset front panel header completely, and I tried switching the power header around. I thought it could be a wake on lan issue, but I disabled that too.

The computer will, effectively, do an improper restart, even though I told it to go into an S3 state. I've also tried doing S1 sleep via a BIOS configuration, but the same thing happens.

Hibernation is completely disabled. So there are no issues with that or hybrid sleep. The same issue will happen when shutting down, also.

I'm out of ideas...

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Sleep can be broken by moving the mouse (at least in some systems) event by a millimeter. What OS are you using? –  Doktoro Reichard Sep 2 '13 at 19:18
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