Looks related to our agent running in 32-bit mode being redirected to a different registry view that doesn't have the data we need.
See: http://msdn2.microsoft.com/en-us/library/ms724072.aspx

Workaround is to create the server by hand:

- From the platform view, click "New Server"
- Select "SQL Server 2005" from the dropdown list
- Click "Configuration Properties" if the server is installed as a named instance change service_name to: MSSQL$YOUR_INSTANCE_NAME
- Check "Auto-Discover Databases?"
- Click OK

To determine your SQL Server's Windows service_name:

(Windows) Start -> Administrative Tools -> Services
Right click the SQL Server service, select Properties. On the General tab, use the value of 'Service name:'.

For a named instance, this will be Service name: MSSQL$YOUR_INSTANCE_NAME
For the default instance, this will be Service name: MSSQLSERVER