I had a similar issue where both hibernation and shutdown took too long on a carpc installation (which was problematic because the powersupply shuts off power completely 2 minutes after the ignition signal goes off, whether the computer has finished shutting down or not).
I did a system restore, and disabled all hibernation and memory pagefile settings, rebooted to let the changes take effect, and then re-enabled them. That seems to have solved it so far (problem hadn't come back in a month and a half).
Give that a try. Even if you don't use hibernation at all, maybe enabling it, and then disabling it will clear up some cache that is used with the memory-cleanup that's done before shutting down.
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