checking/adjusting valves couldn't hurt. you should be coming up on your third check at 12k. if they've never been done, I would say it would be a good idea to check them, regardless if they are the cause of your problem or not.
http://faq.ninja250.org/wiki/Do_I_re..._6000_miles%3F
if you're saying the air leak isn't the cause of your problem, I go back to clogged pilot circuit passages as a possible source.