Hi,
I'm a bit confused, however it does sound like the 2nd instance was installed in the cluster group.
Do you have access to Cluster Admin (Start -> Run -> Cluadmin )? What do you see when you run this? How many groups do you see?
From the sounds of it, you should have about 4 groups
1. Cluster Group
2. Virtual SQL Server 1
3. Virtual SQL Server 2
4. MSDTC
The 'Cluster Group' usually only contains 'Cluster Name', 'Cluster IP Address' & and a cluster disk for the Quorum.