i noticed this happening to me when i was engine braking a lot. so now i just roll up to a stop and click it back to first. and that seemed to solve the problem for the most part. if thats what is going on with you. but...im a new rider and i might not be letting off the throttle all the way when shifting/downshifting so im just getting used to it.
I have been doing a lot of engine braking also. Did hear anyone saying it would cause a problem. I'll stop and see if it gets better.