I called Dillon Tech support on Tuesday and spoke to I thought a Tom, was told today there is not a Tom that works there. Anyway it was late and he wasn't really sure what to do about my problem but took down my info and said someone with some more experience would be contacting me soon to help me with this issue.
Two days later I hadn't heard back from Dillon so I called again and spoke with Steve who was very knowledgable and helpful. He walked me through several troubleshooting steps, most of which I had already tried. He then asked me to check the primer punch to see if it was flush and sure enough it was sticking up quite significantly and we believe that to believe the reason the index arm was not moving like it should. So he is going to send me a new small primer punch and indexing arm, as both the ones I have are now bent.
Hopefully in a few days I'll be able to report that my 650 is back up and running.