--snip--
Also, take a good look at the logs /var/log/messages and dmesg for hard drive errors. Lots of times a bad drive will cause controller bus resets that happen intermittently ... that can cause a 5-10 second delay and then things seem to work fine till the next time.
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I should have mentioned that.... /var/log/messages, /var/log/secure, /var/log/dmesg, /var/log/audit/audit.log.... well, any log I could think of - none show anything out of the ordinary.