I was also running into this problem with Fedora Core 9. The exact problem that I had was as follows:
1) Boot my system
2) Login to Fedora
3) Clock is off... I set the clock
4) Reboot, go into BIOS, and time is OK
5) I boot into Fedora and during boot up (not shutdown) my clock gets screwed
To keep the time consistent I changed the third line of /etc/adjtime from "LOCAL" to "UTC"
After this update I no longer run into problems.