If you have experienced problems trying to integrate YouTrack with LDAP, go get the latest YouTrack bugfix update, YouTrack 1.0.3.
For details on what was fixed and how you should configure LDAP, see description and comments at JT-2779.
You might ask, what are the other improvements that this new bugfix incorporates? There are none, so feel free to treat this as YouTrack 1.0 LDAP Special Edition.
Happy user access!