I found this in the release notes for vCenter 5.1.0b :-
vCenter Server domain admin users might not have permission to login to vCenter Server if upgrade is done using Simple Install
If you use the Simple Install method during upgrade, some vCenter Server domain administrator users who had permission before the upgrade might not have permission to log in to vCenter Server after the upgrade. This happens if vCenter Single Sign On fails to discover some identity sources.
Workaround: Use the Independent Install method. During upgrade, the installer provides a list of users who have vCenter Server administrator access and a list of users who will be deleted.
Link to doc is http://www.vmware.com/support/vsphere5/doc/vsphere-vcenter-server-510b-release-notes.html#resolvedissues
Can you remember which method you selected ?
Please check which specific version you have upgraded to and if it is not v5.1.0b, maybe it is worth upgrading to this version and use the workaround.