Very possible you did not cut enough off of the pto shaft... If this is the case, you could be doing serious damage to your tractor's PTO driveline.
Remove the PTO shaft from the tractor side, remove it from the other shaft that is connect to the tiller. Drop the tiller onto the ground. Without putting the PTO together, reconnect the tractor side PTO shaft and line it up NEXT to the tiller's PTO shaft, you should have a few more inches before they bottom out (since the tiller will dig more into the soil, thus making the shaft shorter). How much overlap do you have?
Is the tiller new?