I found the solution to the problem after some more searching and looking through the github repo of files. The issue is in how the ADC mux is used on the due and this has been fixed in the latest source if you download and build that yourself. The analogRead function was enabling a channel but then did not disable the channel that was enabled after completing the read. This is why the analog Read would always default to one pin over the others since it was looking at which channels were enabled to be read.
Go to git hub, download the source code, and build it yourself to resolve the problem. This will probably be resolved for everyone in the next beta release or when they decide to make the beta part of the stable main release.