I had the same issue with my Upgrade due to a Western Digital green drive. Those Green drives have an boot issue due to the Intellipark feature on those drives. If you're using a Western Digital Green drive you may need to run WDIELE3 /d to disable the Intellipark feature. I had to for my upgrade.
See section 29 in the link for instructions:
http://www.tivocommunity.com/tivo-vb/showthread.php?p=5616160#post5616160
See section 29 in the link for instructions:
http://www.tivocommunity.com/tivo-vb/showthread.php?p=5616160#post5616160