Have you tried shooting the bare shaft with a very high nocking point, maybe 7/8", and a higher than normal brace height, maybe 1" over normal, just to eliminate the possibility that the bare shaft might be rebounding off your arrow shelf and giving you a false indication?
What is your actual draw length and what is the recommended draw length range of the 54" bow?
From my own experience, a 2016 shouldn't be that far off for your 50 lb bow, depending on what actual pounds you're drawing, so I'm kind of puzzled too, just fishing around for an answer.