The fact that re-doing warp zones reduces your time is a bug, but it corrects itself when you launch the game. Every warp zone you beat adds 15 seconds to your time (5 for each level) regardless of the time you took to complete it. For some reason beating them again sets the time from 5 seconds each to 0, but since the time is set by the fact that it's beaten and not the actual time, the game automatically fixes it.
Oh wow, thanks a lot!
Good to know.