I normally use CCI 500 primers in my .40S&W loads but ran out of them and decided to try some Winchester Small Pistol Magnum Primers instead of going to the store.

Usually you are supposed to back off the powder when changing any component in a load but I decided to forgo that procedure and load up to the same specs as before. Same bullet manufacturer and bullet weight, same powder and amount of charge, same brass. I went out and shot both loads over the chronograph expecting to see an increase in the Winchester Small Pistol Magnum primer loads using as I was using Power Pistol for the powder.

The results were surprising!!!! The CCI loads were averaging 13fps faster in one run and 49 fps faster in another run. Just the opposite of expectations.

Anyone have similar experience???

Your experience is not uncommon. "Magnum" primers of one brand may not be as "hot" as standard primers of another. Also, the duration or temperature of the primer's flame and other factors may cause slight variations in velocities that seem counterintuitive.