What is com_set_option?
It probably means that you ran a lot of commands that start with "SET something = somethingelse;"

I would say to set your general_log on for a short while on your dev environment and search for SET commands. It would probably be something to do with setting the server time.

http://dev.mysql.com/doc/refman/5.5/en/server-status-variables.html#statvar_Com_xxx