My Marlin 60 semi-auto does not shoot right on the first shot. It's got something to do with the difference between closing the bolt manually and automatically. I just pop a shot off in the dirt before hunting.
With your bolt action - load a clip, insert, bolt shut putting one in the chamber, and then bolt the gun feeding a new round. Now see if the first shot falls in the same group. Could be the angle of the top round and how it hits the feed ramp.