I have the same Lionel Y3 with Railsounds 5. Its on my hit list to get upgraded to 4 chuffs. Currently its still all stock with 2 chuffs and I have the same exact problem. At very slow speeds the smoke puffs in sync. As it starts to speed up, it starts missing a puff sporadically. Eventually it will only occasionally puff. Stopping the loc and then starting it again, resets the smoke puffing and the same thing will happen again. I'm interested if you figure out what the cause is so I can fix mine.