The problem is that Linux by default sets the system clock to UTC time, while Windows sets it to local time.
As far as I'm aware, Windows doesn't make a distinction between system clock time and local time; there is thus no way to have Windows set the system clock to UTC, short of actually telling Windows your time zone is GMT+0.
You will therefore need to configure your Linux installation to set the system clock to localtime, which can be done via the
hwclock command -- see the manual for exhaustive detail, but in general, the following command should serve:
hwclock --set --localtime --date="5/31/2013 12:34:56"
(You may also, more conveniently, be able to issue
hwclock --systohc --localtime, to copy the system time to the hardware clock and clue
hwclock that it's to manage the hardware clock as local time instead of UTC; on that point, you may also need to edit
/etc/adjtime to let the system know that it shouldn't try to treat the system clock as UTC on startup and shutdown.)