http://seer.entsupport.symantec.com/docs/281824.htm
One of the things that BackupExec has managed to make more difficult than it needs to be is to change the physical location of the database files used in BackupExec. You would think that if you change the location of the database files inside of SQL Server that this would be enough however you would be mistaken. There is a registry key in the above mentioned article that you need to tell the BackupExec service where these files are located. I still am not quite sure as to why you have to do this, but if you fail to do it the files will automatically be put back to its original location.
I ran into this during a SAN migration recently where I attempted to move my BackupExec database from a local C drive over to the SAN. After moving the database files and starting up the database to confirm the move had taken place - BackupExec happily changed everything I had just done. After some head scratching I found the above article which mentioned the magical registry key.

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