Make sure you check out your /etc/lilo.conf and look for a line which says boot=/dev/xxx. If you want it to write to your MBR (that's where you want it) make sure it says boot=/dev/hda , not /dev/hda1 or /dev/hda2 or something (if on your first disk, or /dev/hdb or whatever, whichever disk is booted first.
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