Victor:
Was this an upgrade? When you install Backup Exec, it gives you the option to select what SQL instance to use. Did you select the other server?
One thing that you can try in order to move the BEDB to the local instance is using the Beutility.exe selecting the option to "New Backup Exec Database Location..." and point the DB to the local MSDE.
Regards,
Sandra Rodriguez
Advanced Technical Support Engineer