Brian, this happens still, even with for instance Hardy+Vista
combination. Windowses seem to use local time set to the hardware clock
whereas at least I usually have UTC on the Linux side. Every visit to
Windows and coming back really does move clock for 2 hours (I am at
UTC+2).

What I would do is to use NTP to sync the Linux clock asynchronously at
the bootup after networking, ignoring problems with too high clock skew
(I have seen some setups start syncing to the nearest full hour.. It is
really irritating.) to make sure ntpd/ntpdate does not get confused.
Doing that is not bad imho in any case even if you don't dual-boot.

-- 
Windows dual-boot can corrupt system clock even if time servers are enabled
https://bugs.launchpad.net/bugs/97722
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