I am getting the exact same error message.
My old motherboard died and I just had it replaced. FC3 seemed to handle the new hardware fine, but when I try to boot up I get that error message when it tries to mount the /home directory:
fsck.ext3: unable to set superblock flags on /home
running file system checks just gives the same error (of course, since that is what the boot process was doing when the original message appeared). It seems to happen right after trying to get the 'journal' for that directory. The preceeding line is:
/home: recovering journal
So how did you fix it?