Remember the GPS indicated speed can be off a bit too. Especially with heavy tree cover (or tunnels). It is just a calculated average.
I'll toss another monkey wrench out here- is the odometer in sync with the speedometer? i.e., if your Gen one bike is off a bunch, is the indicated mileage off too? From my rally days- I could make very close approximations of checking both accuracy of speedo and odo, by using the mile markers on the interstate, and a stop watch. Drive at an indicated 60 mph. Now time how long to cover ten miles on the interstate, being very careful to hold your speed steady. (did it take exactly 10 minutes?) Then, using your odometer (interpolating to 1/100 of a mile as best you can) see what your bike measures for the next ten miles of markers. I know most of my cars are off a fair amount, on both measurements. My bike is off too, knowledge gained from warning radar signs.