As one of ACA's legion of volunteers, I have produced many of the GPS routes. I can tell you a bit about the process and how differences arise. In a nutshell, the authoritative data are on the maps as amended, first by the addenda on the ACA web site and then by the Temporary ACA Route Road Closures forum group and the Twitter feed.
Upon reprinting a map or making a significant routing change, Jennifer sends the paper map out. We return the GPS revisions, which she submits to the web site. Occasionally, she changes the GPS data herself. The time that this takes is usually why differences arise. Look in the "About" file that accompanies the GPX files for the version number of the map that we used to make the GPX files. You may need to revise a few waypoints yourself from the addenda.
Simple human error happens, too. I have spotted a few problems, mostly on new routes, when making the GPS data. They get into the addenda quickly. Jennifer reviews my submissions for mistakes as well. Together, we do pretty well, but some updates might still fall into the cracks.
Later today, I will look at the differences you found and write back.