I submitted a bug, and heard back that it may be linked to a quotas kernel bug.
They recommended that I upgrade to 6.0b3.
Fearing what would break (userpanel, etc.), I installed on a test box. I restored the base OS first and then transferred over the /etc/group, /etc/password, /etc/shadow, and /etc/samba
I checked and all my users seemed to be there and the test accounts map, etc. I then restored the /home directory and checked the quotas in server-manager from time to time to watch progress. I was encouraged by the fact that the account totals seemed to be corrrect.
After about 500 users, some of the early accounts started showing 0 for the files owned by the user.
I then did an upgrade to 6.0b3. The upgrade went smoothly, and my userpanel was broken, but other things seemed to be working correctly. I didn't do much testing here, but just a quick glance...
The quotas still show totals for a few users, and nothing for the majority.
"repquota -a" seg faults immediately and no longer gives a partial report of early accounts created.