The Oracle and SQL Server cartridges should be upgraded through the Database cartridge wizard and not through the Agent Manager page.
The FglAM native agent status upgrade process is accustomed to deploying a .gar file, unpacking it, shutting down the FglAM, replace the old code with the new code, and then restarting the FglAM using the newer cartridge code. This should work find for most database cartridges (DB2, Sybase, etc) and "Core" agents (like Infrastructure).
The SQL Server and Oracle cartridges have a two step process, the first to upgrade the SQL PI repository, and the second to deploy the cartridge to the FglAM. The issue that was encountered was more of a warning rather than an error because the process could continue and we could run a groovy script to upgrade SQL PI.
The Agent Managers upgrade process of the SQL Server and Oracle cartridges are not our recommended way to upgrade those two cartridges. From my understanding, this type of upgrade has not been QA tested and there are no plans to test this method at this time.