Vivek,
I had a internal system, and just helped with a second system that use the file system connection to valuate users on the Domain. For Agentry Servers that have multiple backend ends (Note the one below has 8) you need to set the key "enableAuthentication" and "enablePreviousUserAuthentication" for the system connects you want users to be valuated with set to true, all other ones needs to be set to false
Below is the file section that was used:
[File-2]
name=File Back End
allowPreviousUserLogin=true
enableAuthentication=true
enablePreviousUserAuthentication=true
tempPath=
userDomain=Dev
note "Dev" was the domain name with the Active Directory the users are in. Using the file backend makes the Agentry System call out to the OS and that will valuate users. Note if you are running the server on Linux you have do some changes around "pam" but I don't have that information with me.
One system that I had setup to file domain was moved into a DMZ and no longer had access to the Domain. Bill Froelich had some set of Java Code that also calls out to an Active Directory system using a Java System connection. I resolved some issues for it for an internal system but code is too rough to present in its current state. If you need be I can work with Bill and see if we come up with a version that we can post a blog on.