yeap... Motionbased, MapMyRide, and Allsportgps (the one I use most) tent to "smooth" out your path by filtering out the jagged (or corner cutting) path your gps thinks you took. IMO Motionbased does a better job at it then Allsportgps. Also, all GPS devices use different filters specially when it comes to climbing or change in elevation of terrain. Those filters also are used differently based on how good of GPS reception you had. If the gps reception was not very good you see more jagged paths. When you load to a website like the ones mentioned, each one uses their own method of factoring in elevation changes from the USGS. That also "adds" to your travel path making it a bit closer to what you actually traveled.
To this day, I still use my Edge 305 and my cateye computer on my 26er. I only use the Edge on my SS since the wheel size is different and is a bit closer in the calculations. You can run a wheel computer next to your Edge for a while. Play with the changes of wheel size on your Edge until the calculations are a bit closer to the actuals. This may help on normal days with good GPS reception. But it will be off again on bad GPS reception days.
For those not using a GPS are probably thinking, why would I want to spend $200/$300+ on a gps bike computer when I can get better accuracy on my $60 cateye wheel based computer. Well, there is more to it then just GPS reception. Other then calculating speed and distance travel, the GPS device can be use in many, many different ways. I use it for training and tracking work outs. It has also saved my butt on several rides where I've gotten lost. The gps devices got me back on track. You can saved predefined routes (very popular with roadies) or other people's routes and follow them. you can run a "virtual" partner using a previous run of the same route you did before and measure yourself against it.
Enough already.... I could go on and on justifying my needs on this expesive toy (Garmin Edge) but you are probably bored by now ....