If you have worked up a maximum load, using standard primers, when you switch to magnum (or any other) primers, I would back off a grain or two and work back up. Chronograph data generally indicates about 1 grain difference in powder to achieve the same velocity. The pressure curve is also being altered: magnum primers have a hotter flame, of longer duration. The powder is being ignited at a different rate. I am always cautious of any substitutions.
If you are having delayed ignition, I would look hard at the sizing of your brass. You could have a "short" belt on the brass, and a "long" belt in your chamber; both are made within "tolerances". It could easily be a bit of slop, allowing the cartridge to slide forward under impact of the firing pin, resulting in erratic ignition. Try neck sizing some fired cases, and see if the problem goes away. If it does, then adjustment of your sizing die should take care of the problem, as well as extending your brass life.