this can be solved by cleaning up old members in your database.
The reason for this occurring is that when you have over 1000 members, buddy-add refuses to actually work, thus your guild bot can't track the new people.
Running a large guild myself, I've written a little module to clean this up myself but its a little messy, so I haven't released it. It will also delete members that you used !member del on too. I'll post a cut-down version of it when I get home from work tonight.