I've seen this in a couple of upgrades from 961 to 10.2 with instances running in Windows/SQL Server. Open up a case with Informatica and they should be able to provide you with steps and proper scripts to clean the repository metadata to remove versioning.
Quick question - did you ever use versioning in the 961 repository?
Its due to a corruption in your Repository . Please open a case with Informatica support to get the right queries to cleanup the metadata
No idea how exactly you performed the upgrade, so there MAY be one way to get rid of this situation:
Create a copy of the 9.6.1 repository, e.g. via a repository backup and restore to an empty DBMS schema.
Then remove the additional repository service but leave DB contents intact.
Now create a new PowerCenter repository service in 10.2 pointing to the DB schema holding the copied 9.6.1 repository.
The Administrator tool will now ask you to perform an upgrade.
That should work.
But as you have not explained how you did the upgrade, I cannot know whether this is what you have done.
I personally have seen a lot of instances where the issue is not really with an upgrade or the steps followed for the upgrade but rather due to a corruption that persists in the repository.
The best way I would suggest is to contract Informatica support to find the corruption in the repository and have it corrected.
Done the same .