Don't know, but sounds like a case for using external authentication if only to reduce the total number of accounts.
philmodjunk is right. External Authentication is the easiest option.
I have had similar experience. Once user numbers get high, you should avoid using the Security dialog box. I'd be very worried about the potential for file corruption if there was any network dropout while saving user accounts back to the server.
If you cannot use External Authentication then build a table that is used to keep track of user account names and their privilege set. Add scripts that manage user account settings: Add, Enable, Disable, Delete and Change Password. If you are doing this for a single file, it's fairly easy. If you need to do the same across multiple files it is a little bit more complicated but even more necessary.