I would suspect rim thickness / rim cut depth.
8,000 current production NSI 688 primers have functioned perfectly for me over the last year and a half in a variety of guns including a K-20, Browning target guns, Berettas, a Rizzini, and several automatics. Zero misfires.
I did identify 3 missing flash hole seals (green) in the primer tray and did not load those primers. I've had this with Win 209 also.
I just bought 20,000 more NSI 688 and highly recommend the primer.
Winchester primers being a loose fit in current production Winchester hulls? Color me skeptical...