The difference in height is the same as the difference between the recorded height at the start and the end of the ride. I think this is to do with change in atmospheric pressure over the two hours of the ride.  Or it could be that the Green feels like it is higher when the end of the ride is uphill and the ride has been hard. Obviously more research to do here and Debs has kindly offered to help with the data analysis although she recons it can all be done by feel . 
   

As for plotting routes, Google Earth is OK (they call their routes tracks) and has the advantage that you can save/export to Google maps and others. I have not really used others as I have Tracklogs.