In regards to Omega's server install, I can assure you that the problem does not reside with the files themselves. Many have used this set to get their server going without flaw, including a few I have set up for other when I did not have access to my own.
It does indeed seem as though you have the dupe fix running, as this is a common matter with the fix. If you look into more, if you do indeed have it, the time variable for accounts being locked out can be changed.
The original thread on the Dupe Fix touches on this a few times. While the actual dupe fix may not be there anymore, the information about account lockouts more than likely is, I have not checked to be sure though.
You'll also want to check to be sure that your SP's are updating the Leave field properly, as taz had mentioned.
I know I just repeated other replies, but I wanted to be sure to include that the time variable for lockout can be adjusted, and that Omega's files do not hold the flaw, but rather the changes to the files themselves.
If you have an issue with accounts being deleted, I would ensure you have closed the remote access to SQL, as again, Omega's files do not have any issue with storing information. You may also wish to check with any others you have granted DB access to, if your ports are in fact closed. It could just be a GM with an attitude issue.