What you are describing, I think is mentioned here:
page 48 & 49
you establish a connection to the database from the configuration page, then it will ask if you want to create (new installation) or update the database (for an upgrade situation)
When you install Orchestrator, it needs a completely unique DB to use as a data warehouse. When you created the Orchestrator Database, you basically made an empty DB ... so the installer is asking to setup all the tables as required. This is normal.
Please ensure that when you setup the database connector for Orchestrator, it is NOT pointing to the exact same DB Name as vCenter. they need to go to two totally different Database (even though both can be hosted by the same SQL Server).