Oh hai, this weirdness is from our transition from PvP rewards being granted when entering the PvP menu, to awarding them in mail.
The current release uses the menu, and new unreleased builds we are testing send the mail.
The weirdness happens when a new build battles against one of your accounts playing on the current build. In that event, if you have pending PvP rewards, it will treat you like the new build and send you the rewards through mail.
Either way you are getting the same rewards, they just appear a different way.