allawayr: Perhaps the thump you are feeling is a joint internal to the tire where the plies overlap, making the tire stiffer at that point. You might not notice it on the road where the contact patch of the tire is fairly extended compared to the trainer which only contacts the tire at basically a single line of contact. Is there a patch on the tire or the tube? It's probably not worth de-mounting the tire to find out, though. Maybe if you ease off on the roller pressure, or increase the tire pressure, you won't notice it as much.