High MySQL CPU usage, queries seem fine, not running ntp
You can have a high load from lots of short queries as well.  Try setting your long_query_time to 0, and force all clients to reconnect.  Let that run for a few minutes and then set it back to your default.  You can peruse the results by hand or use a tool like pt-query-digest.

In either case, you should be able to figure out if there is in fact a bunch going on, just very quickly.