For the record, I've recently observed such behaviour on non-cheap 64bit server harware.
That was Pg 8.4.0. hardware specs available on request.
EXPLAIN ANALYZE SELECT was over 2 times slower that SELECT. repeatedly.
Answering an obligatory question: NO virtualization (vmware/xen/other) there.
Question: Is there anything as normal, accepted level of performance degradation when using EXPLAIN ANALYZE compared to plain query?
Apparently you can force linux kernel to consider different time source, as it sort of guess-probes which one would be the best when it boots. I don't remember the exact option, but it is easy to find on the net.