When your gmaps route is going around curves, you need to zoom way in and click a lot of short distances. It's easier to do this in satellite mode instead of map mode. If you go short-cutting in your map by clicking across huge chunks of land, then naturally your map results are going to be shorter, just as your run would be shorter if you actually ran the giant shortcuts that you clicked.
usatf.org/routes works exactly the same way.
To illustrate:
Here's an example of a clumsy mapping job that is definitely going to come out short. Zoom way in and look at how the map shortcuts huge chunks of ground, instead of following Burke-Gilman precisely, even though following Burke-Gilman was obviously the author's intent. This is especially obvious just north of Gas Works Park.
http://www.usatf.org/routes/view.asp?rID=4716
Now, by contrast, check out this map; zoom in in Satellite mode and observe how the curves around the Shedd Aquarium and the Adler Planetarium are more or less precisely drawn.
http://www.gmap-pedometer.com/?r=211430
Okey dokey?
Note that this degree of accuracy is harder to attain away from urban areas, where the satellite photos on gmaps do not zoom in as much as they do in the cities. Out in the country you're going to have to trust the map mode. Still zoom in as much as is practical, and follow the curves precisely as you click through your map.