Ive seen the intermittent pulsing red blue server lights before.
The next time it starts doing it. shut down, restart, and RDP into the server and check the event viewer for a recent error. When it happened to me, it was related to an add in conflict.
But since you said you don't have any add-ins, that only leaves the powerchute. if event viewer doesn't offer any clues, try a fresh install of your OS & powerchute. Since you mentioned you've been running the server for quite some time, I'm guessing it might be time to do a fresh OS install. Maybe it's time.
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ex49x/v1 (toyin w/Vail) VGA Q8200s w/two 30mm cooling fans 4gb Ram Rear Casecover Cooling Mod
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