I found a workaround to your problem.
You'll need to add a new permission with the same username but the new SSO domain to your vcenter.
An old user is listed as SYSTEM-DOMAIN\jdoe in your permissions tab (i.e have a look at your full client).
Add a permission for VSPHERE.LOCAL\jdoe and it's working again.
I noticed this while looking at my SSO users in the webclient. All SSO-users (5.1 and 5.5 entries) are listed under SYSTEM-DOMAIN and VSPHERE.LOCAL but the Domain column shows "vsphere.local" for every single entry.
I had a similar issue, albeit not from upgrading a to b. I found that my vcenter server object was missing the propery permissions and that I had to add the vsphere.local\administrators *group* to my vcenter server object. home > vcenter > inventory lists\vCenter servers > vcenter (or whatever name) > manage > permissions.