Hello Gebbert,
If you don't find any difference in the SEPM its better you download the RU6A software from https://fileconnect.symantec.com
Once you have downloaded, extract the files.
Then login into SEPM. Click Admin tab - Install Packages - Add Client Install Package.
Then click browse & go to the RU6A software extracted folder. In that go to SEPM folder - Install Package folder. You will be able to select packages for 32-Bit, 64-Bit & for MAC. Import the packages.
Logout & run upgrade.bat from :\Program Files\Symantec\Symantec Enpoint Protection Manager\Bin
Login back to SEPM & export RU6a package.
Start upgrading RU6a & then upgrade to RU6 MP3.
This should work because upgrading from RU5 to RU6MP3 might cause client communication issues. Hence upgrade clients to RU6a & then to RU6MP3.