FLServer is not a very good program. It gets laggy after a while and after a fair bit of load. Partially this is a result of the age of the game. It's also partially because of the complexity of FLHook and all the plugins that run on the server, many of which don't really do a whole lot of garbage collection at all.
Perhaps one day I will attempt large scale lag testing with regards to FLHook and plugins, in an effort to determine where the lag is coming from so I can fix it.