So what you are saying is, The bolt is not locking back after the last round in the magazine is fired. It could be your reloads are powerful enough to push the bolt back enough to strip a round from the Magazine, but not powerful enough to push the bolt back enough to engage the Bolt stop. To confirm this, try shooting some Factory loads.
Also something else to try, With an empty Magazine inserted, Cycle the action by hand, Does the Bolt lock back? I once had a Bolt Stop with elongated finger on My Colt Magazine lower that was just a shade too short and was not engaging the Magazine follower.