At a guess the 2005 and 2008 instances would be listening on different ports. Perhaps you need to set the connection string for the SQL Server 2008 instance to the correct port; you could be hitting the SQL Server 2005 listener and asking it for an instance that is not present on the 2005 installation.
What port is the SQL Server 2008 instance listening on - This article discusses the subject. and has a powershell script that actually interrogates the system to find out what port the DBMS is really listening on. It also talks a little about where this config lives in the registry.