It appears that /etc/rc.d/rc.sysinit was recently modified to move calls to hwclock earlier in the file. In fact, it appears, that these calls now happen before the root filesystem is checked and remounted read-write. This is somewhat problematic, given that hwclock attempts to modify files on the root filesystem (most notably, /etc/adjtime) when it is called with "--adjust". Now every time I reboot I get hwclock about how it can't modify what it wants to modify because it's on a read only filesystem. Alas, I failed to capture the exact error, but it happens reliably. I suspect you can duplicate it by removing /etc/adjtime before rebooting.
AFAIK, this was fixed in 6.40-1....