You can receive this issue for a few reasons. When you try to configure the Sql instance, we will check for the installed instances from the registry on the server.
A few things to check there is to make sure SQL 2005/2008 backwards compatibility pack is installed on SQL server
also SMO package (comes with SQL 2005 backwards compatibility pack) is installed on SQL server
Also if this is a 32 bit instance of Sql running on a 64bit OS, we will be looking to the 64 registry for the instances, where they will not exist. In this case you will need to install the 32 bit agent.
What version of Windows and Sql?
What version of CV? also, if course make sure the Commvault update have been applied also.
Let me know if this helps.