I recommend getting this:
http://nallar.me/buildservice/job/T...cessfulBuild/artifact/target/TickProfiler.jar
You may have to go into the config for it and turn the permissions part off (or you could just run the profile command on the console).
Once placed in your mods dir, fire up your server, stop server, change config where required, start server up again.
Wait for the hi CPU event to occur, then do (from the console): profile e
It might take a little longer to do its job during the event, but it will happen, then you just look for the things that are taking an excessively large amount of time to do stuff.
Other option is WarmRoast by sk89q (the worldedit guy), which is a seperate jar that runs independent of the game, assuming you have the MCP mappings for 1.6.4 you can use that to also give you an idea of where the issue might be.