I've installed CentOS and Scientific Linux on two computers each with several operating systems raging from Linux, FreeBSD and Windows. When prompted for Configuring the Time Zone I selected the city nearest to my timezone and left the System clock uses UTC checked.
My system clock was fine on CentOS 6.2 and SL 6.2 but when I booted to one of the other operating systems their clock would be off by 1 hour...
According to the Red Hat Enterprise Linux 6 Installation Guide you should only select System clock uses UTC if RHEL is the only operating system on your computer. So to fix things just use the Time and Date Properties Tool and uncheck the System clock uses UTC option. The tool can be accessed running system-config-date as root or pointing to System -> Administration -> Date & Time.
Simple solution for such an annoying problem ;)