I only ever see that message when my system goes out to lunch an I have to hit the big switch to reset it. I get it once, then fschk does its magic, and all is good.
I also once built my kernel without rtc support by mistake, and I then also got that message + a message complaining it couldn't set the hardware clock during startup/shutdown. I also dualboot, so my bios is set to localtime. I'd check in your bios if time is set correctly, then boot up with a live cd, and with your volumes unmounted run fschk on them. Tom
