The most common problem in Halo Custom Edition is that there are players playing on two big versions (v1.00 and v1.09). The latest version has fixed several exploits (mostly DoS) but the only crack that exists is for version v1.00. After v1.08, SafeDisc was stripped from the original executable and thus a CD is not required anymore. Still the majority of pirates are still playing servers on v1.00.
Our goal was to unify both versions into one by having the Halo Custom Edition Dedicated Servers appear on both server lists (v1.00 and v1.09). This is done by having the server switch every interval its own version and afterwards sends the information to GameSpy. It might be for a short period of time that the server will not appear on one of the lists. Our tests have shown though that this small sacrifice still leads to a higher player count inside the server.
For all you trolls: CD Key Check was not removed.