The AC waypoints are off by a few meters in some cases - it will have you turn left and then do a u-turn after a short distance. Just look at the map window and you can see these errors as obvious.
I have seen the same thing. The maps in my receiver, Garmin City Select v6, and the maps used to mark the AC waypoints, Garmin Metroguide v4, do vary by a few meters.
Out of curiousity, I checked several against the gold standard, aerial photos from Microsoft's Terraserver. City Select is almost always more accurate, but not every time. I think the Navteq database used there is newer and better than the TeleAtlas database in Metroguide v4.
The difference is not large enough to affect navigation, but if it becomes bothersome, you can easily move the waypoints in MapSource. Be sure to set them right on divided highways, or you will get some bizarre routes!