How long ago did you do the upgrade on the SEPM? Does the LU content revision count cover up to the dates prior to the upgrade? Have you upgraded the SEP client on the SEPM too?
I've recently noticed that the "Show LiveUpdate Downloads" section of my SEPM no longer lists SEP11 Virus Definitions, eventhough it is still providing updates to SEP11 clients. Unfortunately, I can't tell you what triggered this...
I suppose you should be able to force a refresh of the content downloaded by LU on the SEPM by reinstalling and reregistering LU:
http://www.symantec.com/docs/TECH171060