If you ordered a 64-slot server and run in a game mode other than ConquestLarge0 (Conquest64), then your server will run with fewer slots. For instance, RushLarge0 is a 32-slot mode, and the game auto-adjusts for this. (TDM is 24 slots, SQRUSH is 8.)
If you don't use our map cycler (and instead specify a traditional one manually), your server will run at the smallest number of slots supported by any game type in the cycle.
If you do run our mapcycler, and it cycles to a game mode supporting fewer slots than the current one, extra players will be dropped.
Additionally, if you upgrade the server, you may need to go to the "Easy setup" page in the control panel and adjust the "Player limit" option upward to match your new slot count.