I've switched the server mod (an un-modified server cannot support plugins) from CraftBukkit to Spigot. In theory Spigot offers better performance (e.g. less RAM used) but it's a bit more complicated which is why I've put it off until now. So far the server seems to be running fine, and it also seems to have fixed the issue with the monsters wondering off into unloaded chunks and accumulating, preventing more monsters from spawning. So Bee might be a little more dangerous now.
However, if you notice any aspect of Minecraft not working as you think it should be, please let me know.
However, if you notice any aspect of Minecraft not working as you think it should be, please let me know.