When you are trying the classicupgrade script, and you are converting a samba3 installation that uses ldapsam you have an object that does LDAP searches but doesn't notice if it gets told the search results have been limited.
This object is created on around line 616 of python/samba/upgrade.py with this line:
s3db = samba3.get_sam_db()
In my case I found that the call to s3db.search_users(0) on about line 685 resulted in a list of users that didn't include everyone. Once I removed the search limit on my ldap server the problem went away. In my case I have more than enough users to reach the default openldap limit of 500.
I think an exception should be thrown if the server hits this limit, so it is more obvious to users that there is a problem.
I think s3db.search_users(0) is implemented in source3/passdb/py_passdb.c on about line 2477. But my C is very rusty, so I can't offer a patch.
Seems to be a valid issue.