Finally, make sure you don't have anything funky going on with the hard drives... I recall a while ago (yes, ok, it was on windows) a HDD dropped into PIO mode and utterly crippled the entire machine...
That brings back bad memories. :-)
Another issue we've had is a silently failing hard disk. It would just lock
the firewall for seconds at a time with nothing out of the ordinary showing
anywhere. Nothing in the logs, normal top, ps etc. It would just become
unresponsive then come back.
So a Neil's ghost to another box is a good idea, it'll rule out flacky hardware.
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Jean-Francois Pirus