The act of upgrading a ConflictSolver database from v3.5 to v5.5 should result in a completly new database being created and the packages from the old database being re-imported into the new database.
Assuming the upgrade process worked as designed, the new database would be assigned a database owner (dbo) based upon the current connection to the database. And, so if you connected to the upgraded database in the same way as you originally connected to the v3.5 database, then everything should have worked.
Ultimately, you need to examine the Users and associated security settings being assigned to the newly created database. If you have AdminStudio v5.5 Enterprise Edition, then the main AdminStudio IDE will have under the 'Catalog' menu and 'Security' option to allow you to view and modify the underlying users and security options for the new database. Otherwise, you can examine and modify these options via the SQL Server Enterprise Manager.
Allen Saxton
InstallShield AdminStudio Development