You said it was a new tire, but a thumping from the rear? My first thought would be a foreign object. It only happens when it's hot?
Try this. Run around until you feel the thumping. Go home. Put the backside up on a paddock stand. Spin the rear tire slow and fast, from the side, watching the tread where it would meet the road. Place a ruler of some other straight object against the stand, if it helps you watch the tread for signs of a "bump."
Doing this, the rear sprocket will also be in your line of sight. Look to see if there's a point where the chain doesn't go around the sprocket like it does all the other time.
What you're looking for is a possible deformation in the new tire, a foreign object in said tire, or a stuck link your chain.
Hope it helps and good luck!