At startup I keep getting a dosfsck "differences between boot sector and backup" error. Now I know how to set it so the error doesn't show, but I'd prefer to remove the inconsistency instead. I've tried to use option #2 (copy original to backup) but it won't work. I get a "Leaving file system unchanged" response. I don't want to put the backup in place of the original because other than the error in Ubuntu the system works fine, so I'm presuming that the problem is with the backup. I've tried running it as su, booting to a maintenance prompt and running it that way, and no go. Nothing related to either Windows or Slackware are aware of the problem, so I can't fix it with something from either of them. What do I need to do to get it to actually implement the correction? I'm running 6.10 if that has any influence on your suggestions.

I have same error before and I don't know how to solve it. Finally what I do is:-
1. Copy entire OS out from Hard disk
2. recreate the partition table
3. copy entire OS back to the hard disk
4. boot into live cd, chroot it, perform grub-install

It take time, but problem solve.
Regards,
Ks

Found out a way around it. I used a boot CD with Gparted to slightly reduce the size of the primary partition of the drive in question. I then saved, rebooted and resized the drive to use up the bit of space I had just freed up. In doing so GParted re-wrote the partition table for both the primary and backup.