SQL DB instances lose backslash

Just tried migrating my fully patched Opmanager backend database this morning from a SQL 2005 server to a SQL 2008 server. My DBA successfully backed up the database and restored to the new server. I ran the DBConfiguration.bat file and entered in the new connection info. My problem is the 2008 SQL servers use instances. I can enter the new connection info and the tool accepts the new server with instance without error. Unfortunately the service fails to start and the logs I find show attempts to connect to a string where the slash has been removed. And when I open the DBconfiguration.bat back up, the backslash is missing.

Ex. Server\Instance saves as ServerInstance

What do I need to do to get this to work?