Patrick,
Its always recommended to run the upgrade utility before an upgrade attempt on the CM server and not before running BARS.
The first step you need to do before running upgrade utility is to backup the servers. Once you run the upgrade utility, the first thing it checks is validate the integrity of the backup tar file.
You are supposed to fix any errors in the outpu tof the upgrade utility before moving forward.
HTH
http://www.cisco.com/en/US/products/sw/voicesw/ps556/prod_installation_guide09186a00806de878.html
Sankar.
Sankar Nair
UC Solutions Architect
Pacific Northwest | CDW
CCIE Collaboration #17135 Emeritus