OK, maybe I am not completely understanding what happened. From what i gather, you installed SQL Server 2005, then installed SQL Server 2000 without uninstalling SQL Server 2005. Correct? If that is the case, when you installed SQL Server 2000, did you create a new instance of SQL Server 2000? It appears that for some reason SQL Server 2000 is using the same SQL Server 2005 instance. I have never had both installed on the same box, espcially in that order, but that is what it sounds like is happening.
I would remove SQL Server 2000, reinstall with a new instance, and try again.