Hi,
just updated a vRealize Operations Manager server today from 6.0.2 to 6.6.1, and unfortunately I got an error during the fourth step of nine (4/9):
Failed The PAK action "apply_system_update" script "/usr/lib/vmware-vcopssuite/python/bin/python updateCoordinator.pu -p " failed
As I was in the middle of a vCenter upgrade and some other stuff, that was a little annoying, and I could not really find any articles on the particular problem, so I did some digging around in the appliance, and it turns out that it is not pleased with the certificate on the appliance.
The certificates was changed to a self signed certificate from an internal Microsoft PKI infrastructure a while ago, and it was still using SHA1 ciphers. So I reverted the machine to the snapshot I took before I initiated the upgrade, booted the appliance, and issued and installed a new certificate, and PRESTO, the upgrade was back on track.
Hope that you found this article useful, and did not spend a lot of time on this issue.