You're not the only one. The below comment seems to suggest there might be an issue upgrading from RU3.
https://www-secure.symantec.com/connect/blogs/security-advisory-symantec-endpoint-protection-management-vulnerabi#comment-9811901
Do you get the same thing? Does the SEPM upgrade complete but stay onf the same version number? I'd be very interested if it's replicable and consistent, as I've got plans to upgrade a RU3 SEPM in the near future.