Hi There,
From what I recall, certain accounts have permissions to query against different attributes.
Are you using the same account when you're looking around with the standalone tools?
If so, then there might be some issue with the query that's being made. I think the builtin logging won't show this granularity for AD communication, but if you're connecting on port 389, you can use Wireshark to sniff the communication with the domain controller, and see the query and any results that are getting passed back.
If you like, you can PM me with the log, and I can look to see what's going on.
Regards,
Cary