Matt, I'll agree with you that GPS is not 100% accurate. Nothing is, for that matter.
But I also have to say, I think the GPS unit you were referencing was seriously effed up. I have never had one do that. On one of my old setups, I did two top speed runs with two different units, my Garmin handheld, and the TomTom from my car. One read 46.6, the other 46.8. They have seperate sections for average and max speed.
I think the only consideration that needs to be taken is the grade of the surface being ridden on; you can easily add a few mph on even the smallest of slopes.