I have an early 397PA ("P" style trigger but has the removable valve). That valve will not come out without some coercion from a dowel tapped by a hammer. Like yours, no damage to o-rings, so I'm thinking no burrs. I wondered if the pump tube is slightly out of round, but if it is, it's not enough to cause any blow-by when pumping. It pumps up strong, and is VERY accurate, with almost any pellet.
That IS strange. I've rebuilt probably 30 different models all the way back to the Streaks. Never had this issue with the cartridge valve guns, a la Crosman manufactured. Make sure the bolt assembly is removed. The cocking lug falls below and will cause valve removal woes. Very strange. I've personally never had this issue.