The hot rod is only active for the first 5 minutes of the cycle. So if the cooker stays on and you add pellets after the fire has gone out, there is nothing there to start the fire. You can still start on smoke as always, but if you run it out of pellets, you will have to turn it off, turn it on and prime it by feeding pellets down the auger. Then when they are dropping in the firepot, turn it off as the hot rod is probably done with its cycle, then turn it back to smoke to reignite the pellets.
The easiest thing, is just to make sure you don't run it out of pellets.
