Question: Watney digs up the plutonium and places it in the rover. Why is the rover so cold later after the HAB blows up?
Answer: He used the RTG to warm the rover on his trip to get Pathfinder. Once he returned he buried it again, since it posed a radiation hazard.
I rechecked the book. He did NOT rebury it. In fact, he tore out extra insulation inside the rover so the interior would not get too warm during his upcoming trip to the other landing site. The RTG was, in fact, an integral part of his equipment for the journey. However, by tearing out an appropriate amount of insulation, he pointed out that the heat from the RTG would leak out some during regular operation. But sitting unoccupied for a while, enough heat might have leaked out to make it chilly.
Answer: Is that mentioned in the book? Don't remember it being mentioned, but I can recheck.
Answer: Watney used the RTG to heat the Rover for the trip to get Pathfinder. When he got back, he re-buried the RTG because he didn't need it while at the Hab (not travelling long distances) - hence the cold scene you noticed. Then later, when he goes on the even longer trip to the Ares 4 MAV, he digs up the RTG a second time and brings it along.
Aerinah