It sounds like you are using Project Manager to connect to a Methodology Management database.
You will need to make sure you use Project Manager to access your PMDB database and Methodology Manager to access the MMDB database.
If they aren't named as obvious as PMDB/MMDB then you can check the database version, this will also show the database type.
You can run the following query - the first four characters should be either PMDB or MMDB. (Exception to this would be an 8.x Professional Project Management database which will show PPMDB)
I did run that query yesterday in SQL Server Management Studio Express (logged in as privuser) for the affected database. It did not return any result, although the query was executed successfully. Other queries (such as listing projects) also yielded no results although they were executed successfully. Really weird.
Thanks for your help!
The only thing I can think is that you are looking at the 'Messages' tab in SQL Management Studio and not at the 'Results' tab which shows the actual detail from the query.
The prefer table only has a single row in it so it might be easiest to just open that table up and scroll across to find the database_version field.