Ubuntu has set the system clock to UTC since the Intrepid Ibex (8.10.) I didn't notice because I had upgraded through several other versions. Using UTC for the system clock is cool if you don't dual-boot, but I do. The functionality exists in at least Vista and later to use UTC for the system clock, but I'm using XP and don't trust it to work even if it appears to.
The fix is to edit the /etc/default/rcS file and change UTC=yes to UTC=no and reboot. From then on, Linux will store the current system time in the real time clock. Make sure that all operating systems are fully updated so that their time zone calibration matches; if you have an outdated Windows XP system it will disagree with Linux about when daylight savings time occurs.