I've had this happen, too. In my case, it was a AFP (Mac file sharing) based home directory server and an Open Directory Replica. I ended up reinstalling the OS and re-binding it to the OD Master. Nothing else seemed to work. Not disk repair tools (fsck, diskutil, Disk Warrior), or re-binding to the OD Master, or software updates, or checking the logs, or calling Apple more than a half-dozen times.
If this is your Open Directory Master, export all your users, user groups, computers, and computer groups via Workgroup Manager. Then demote all OD Replicas to Stand Alone and reboot them. Then re-import the Workgroup Manager data and re-bind the Replicas. (Note that all users' passwords will be lost. You can use the shareware program Passanger to read the users export and re-write it with known passwords. Then distribute the passwords to your users.) This process will cause the Open Directory data to rebuild, which should remove the corruption in an OD Master. Yes, I've had to do this a few times before. My users were... unhappy about the experience. They were glad that they could login again, though.
If your server is at a school, don't forget that Apple provides free phone support.