I have an OS X 10.6. server that I have created 400 users accounts on. It is configured as an Open Directory Master - Home Accounts were created with LDAP and can I see the Home Accounts on the share - but cannot login with the created usernames. It is a fairly simple setup in that the users only need to connect via AFP for simple file transfers. I have other OS X servers that are Stand Alone, and do not rely on LDAP. Perhaps there is something basic I have missed in setting up the accounts?
I don't know Passenger (what is it?), but it's likely you haven't created all necessary LDAP attributes and password server/Kerberos entries when importing your users.
Open Directory needs a set of Apple specific attributes to work correctly, so maybe try if everything works if you create a user from scratch in WGM.
Do you have service access control turned on? 10.6 server turns this on if you use the "Create Users and Groups" option in the initial setup. You can check and adjust it in Server Admin -> server name in sidebar -> Access in the toolbar -> Services tab below that -> AFP service in the list below that. You can either add users and/or groups to the access list, or just enable the service for all users & groups (that option is above the list on the right).