This is indeed interesting !
I have never experienced such an issue with the update_prebinding command of Mac OS X. However, sometimes, it can experience difficulties when trying to update the prebinding on a file that is heavily damaged or corrupted.
You may want to see at which point precisely the command experiences issues and if the same problem happens on a clean install.
Would it not be the case, you may want to repair or delete (if possible) the affected file.
You may want to post on the UNIX forums of the Apple discussions where you will find many experienced users who will be able to help you troubleshoot this issue in more detail than we can do it here.
Let me know if this helps !