I pretty much expected there to be some discrepancy, if I found two GPS unit reporting the same thing I'd automatically think one was faulty.
Because I ride in the dark I can cut many of the corners to suit myself, it only takes a few cut corners and a few minor GPS signal hiccups over 10ks to see significant changes in the data.
So far the watch is slightly better at plotting the path, it hasn't had me riding off the road and into people properties, where as MapMyRide and Google both have instances around here where it tells me I crossed over a property boundary and through a fence while taking a wide arc around a corner.