Grub gives messages about the boot sector being used by other software. What should I do?

It's not a big deal since there is no error reported so just warning.

But, if you wish to get rid of this, you need to wipe sector 32. To do this you have many choices:

a. Wiping the whole hard disk;

b. writing zeros to Whole sectors in your MBR and reinstall your grub;

c. Writing zeros to sector 32 in your MBR (that's what we'll do here).

To do that follow the following steps:

1. Backup your MBR:

   sudo dd if=/dev/sda of=~/first_63_sectors bs=512 count=63
   

2. zero your sector number 32:

   sudo dd if=/dev/zero of=/dev/sda bs=512 count=1 seek=32
   

3. chroot and reinstall grub: Here "/media" should be whatever your chosen mount point is. Some step-by-step instructions use "/mnt" rather than "/media".

   sudo mount /dev/sda* /media/sda*
   
   sudo mount --bind /dev /media/sda*/dev
   
   sudo mount --bind /proc /media/sda*/proc
   
   sudo mount --bind /sys /media/sda*/sys
   
   sudo chroot /media/sda*
   

   PS: replace * by the appropriate number of your hdd

   Now update your grub:

   sudo update-grub
   

Note: You are not obliged to these steps, since its not an error that may affect your system.

I found a couple of useful links that explain what the message is about, and how to clean out the boot sectors on the disk. This thread gives a very good explanation of the problem. This thread gives a nice easy cookbook recipe for cleaning things up.

The cookbook worked for me, although I made a mess of the chrooting bit... (see below)

I am lucky in that my computer is single-boot and I have no plans EVER to re-install Windows. But it seems that if you have a dual-boot Windows system with software that uses FlexNet or similar software, you can expect to have regular problems. Also I think some Windows viruses may use this part of the disk. The first thread discussion offers a solution for Ubuntu users, to install an app called boot-repair on your live-CD USB booter.

I also found the boot-repair program referred to above invaluable when things go wrong. IMHO this is so useful it should be on the Live CD by default. See this link.