Every morning at 5AM EST BanManager throws a connection leak detection error and either A) Crashes the server or B) Spams the console with errors and causes everyone to time out.

http://pastebin.com/Dsu4wUhZ

It means you have a slowdown in your database. Are you running backups at 5am?

Yes, actually, I do a MySQLDump at 5am.

By default, mysqldump will lock tables, preventing reads and writes, hence your timeout problems. This is not an issue with BanManager. The exception simply made you aware of the problem.

Interesting. I also do dumps hourly but have no issues like this. Actually I am not sure if you are right, @confuser. As far as I read about that stuff is that you can do dumps while data is in use but these dumps may in some rare cases not be 100% functional.

So beside those hourly backups I also make a full backup while the server is stopped. So I can safely so things like flush tables with read lock; to make a clean dump and later unlock tables; again.

@EvilOlaf There are different options when running the command in which this can be avoided; however by default this scenario is what occurs.

Please also note that BM uses MySIAM tables for a reason, and switching to InnoDB (which you may have seen recommended in a lot of places) may cause issues when syncing.

This is more of a general sys admin issue rather than specific to BM.