Ubuntu Boot Error: “differences between boot sector and its backup”

I have my Acer Aspire laptop dual booting Ubuntu Linux with Windows XP but, despite being sympathetic to Linux and interested in learning more about it, I don’t use Ubuntu very often.  One major reason for this was the amount of time it takes to boot up.  Over time I noticed an error message and looking at it began to suspect that this error was partially responsible for the long load times.

There are differences between boot sector and its backup
… [sequences of numbers]…
Not automatically fixing this

According to this forum thread, it seems like this error may have been let loose when I changed the grub configuration to make the OS names a bit more user-friendly and have the system stop booting into Ubuntu by default (the girlfriend isn’t converted yet and even I preferred Windows for regular use). This seems to affect the MBR, which doesn’t overwrite the backup and therefore causes the above problem.

SimonU at UbuntuForums had the same problem on his Ubuntu laptop and posted a solution which I decided to borrow.

sudo cp /etc/init.d/checkfs.sh /etc/init.d/checkfsbackup.sh
sudo rm /etc/init.d/checkfs.sh

I had already hit the button to restart my PC when I thought to myself “I really should have looked at what it was doing  and made sure it was doing it to the right hard drive for my system” and started worrying that I may have just made my machine unbootable. Luckily all was ok and my laptop now boots into Ubuntu in a fraction of the time it had taken before. If I could only figure out how to stop Ubuntu overheating the laptop so much and causing the fan to run at full pelt, I’d maybe use it on a regular basis.

If that doesn’t work for you another thread talks about skipping the file system check (fsck) on FAT32 drives as an alternative solution.

Author: nerd.

An experienced IT professional, I used to run a number of small websites and spend a lot of time tinkering with my sites or my PC - back when I had free time.

2 thoughts on “Ubuntu Boot Error: “differences between boot sector and its backup””

  1. That seems like really bad advice to me, you’re removing the symptom with fixing the problem. All it takes is to run dosfsck once the machine has booted up and choose to copy the boot sector over the backup (assuming your machine is booting properly).

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