Re: bike mode, looking at your original plot I wondered if your phone was on walking mode -- like when you're talking friends on the phone outside the bar and walking back and forth. As opposed to driving directions, when it figures you're on the road or street and fits location to the road.

I'd reset the Padrone until you can get to a good calibration road: road that's straight and flat without traffic signals or stop signs, and (the tough part) one with accurately surveyed mile markers. Note your starting mileage on the Padrone and the mile marker, ride as far as you can, and note stopping mileage (Padrone and mile marker). Figure your correction (mile marker distance * current wheel circumference / Padrone distance) and put that in as your new wheel circumference.

(Hope I got that straight!)