Try this just for kicks, I dont normally recommend it, in fact, i ususally
recommend just the opposite. but in your situation it may provide the info
you want.

Fix your machine so the boot sector is the way you want. Then reboot and go
to BIOS setup. Select the antivirus bootsector protection thing and turn
the protection on.

Now reboot and proceed with your normal use. Perhaps you will be notified at
the time the bootsector is being overwritten and then you will know what is
happening.

Again, I only recommend this as a debugging tool to determine how your boot
sector is getting overwritten. Once you know, turn that thing back off.

Eric