Problem has been solved. The problem was me. I did not have 3 check boxes checked in Bossa 1.8 that needed to be checked. I went back and re-read the instructions on DC42's blog and fixed my error. My PanelDue is now updated.
I have it figured out. The reprap configurator set my end stop code wrong. It was set as M574 X1 Y2 S1. It should have been M574 X1 Y1 S1. Everything is working fine now.
Not a problem. The file for this machine was generated last year. I have been running it homing each axis separately for that long. Now I am trying to work out the bugs. Been learning a lot the last couple of weeks between reading and asking questions here.
I now have my x and y axis movement problem solved. I had to swap the x and y motors back to what they were originally. And I changed the M569 P0 and P1 S parameter to 0 on both. Now everything moves correctly and homes correctly. Now I can neaten up the wiring and start tuning settings to get great prints.