It is not recommend to upgrade directly from RU5 to RU6MP3
This migration path is not supported.
RU6MP3 is a Maintenance patch and not a maintenance release, A MP can only be installed on the main build. You can install RU6 over RTM or MR3 or MR4MP2 but not RU6MP3. For that you need to have RU6/RU6a
It is not recommend to upgrade directly from RU5 or MR4 to RU6MP3
This migration path is not supported.
Possible effects after a direct upgrade to RU6MP3 from a lower version [except RU6]:
Schema Corruption.
Possible dll corruption.
Policies Corruption.
Network breakdown.
Challenges with uninstalling SEP.
So what you need Upgrade the clients to RU6 and then upgrade to RU6MP3.