Running version 2006 as well and just installed MBAM last night. I can run the reports from the report server and see the BitLocker activity, the SelfService website works and I can grab recovery keys. However, I can't do anything with the HelpDesk site except load the page. The audit report does nothing (I can run it from the report server), and I can't use any of the recovery pages. The event log complains about the website SPN so I'm not sure if I added the right SPN (http/fqdn of the server) based on Microsofts recommendation for an application pool running under Network Service. I also see WebAppReocveryDbError for 'NT AUTHORITY\ANONYMOUS LOGON', which I don't understand as we're running as Network Service. Also WebAppDbError regarding the missing stored procedure. I don't have ComplianceCore.GetVersion in my database either.
I'll try opening a ticket with Microsoft, as much as I dread those exchanges, but maybe I'll get lucky here. I've done this build at another employer and had no issues, but this deployment is troublesome.