SEP 12.1 RU2 includes a new feature for GUPs functionality:
https://www-secure.symantec.com/connect/articles/sep-121-ru2-and-explicit-group-update-providers
http://www.symantec.com/business/support/index?page=content&id=TECH198640
...according to the documentation after SEPM Upgrade to 12.1 RU2 - GUPs does not need to be 12.1 RU2 in order to work properly - although the differences between 11 and 12.1 are quite steep and an upgrade would be highly recommended.
One other thing you can try is to delete the old Liveupdate Policy assigned to clients and gups and create a new one - offen happens that the policy gets corrupted during the SEPM upgrade and then cannot be properly read by clients.