Hi,
I don´t know direct answer to your question, unfortunately, but I have a problem finding these 99 folders in my client machines… 
I´m running a small computer lab (15 machines) user homedirectories on a 10.4 server (ldap+kerberos) over 100Mbit ethernet.
Resently on the client machines I have started to find folders named 99 on the same level that Users, Applications, System, etc…
I can delete them as a root, but they appear back soon.
I was also browsing through my user accounts with workgroup manager and I found out that in the info panel there, all the users last name was 99
Duh, I just wonder if this is some “feature” of 10.4 server?
Go figure…
Sicerely, Antti
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