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You can fairly easily switch directory providers, so you could just try that and see if it works. A lot of organizations will have a dedicated ProGet test instance (note this requires a separate server license) to test upgrades and major configuration changes.
For most organizations, both LDAP and the Multi-domain configuration "just work". So long as service account running the ProGet web application has the appropriate permissions to query, and the domains are set for proper trust, then users will be retreived as expected.
But for some, it doesn't, and the only way to find out why is to do a detailed analysis using our code. 90% of the time it's a domain configuration problem. But there's no easy way to identify it because the AD libraries do not tell us why certain users or their groups are not returned in a query.