I call most of my pages using changePage() not sure if leaving the data-role"page" will work that way. Anyway, I changed my jqm link to the CDN and it is working now. I didn't know that any changes were made since the 1.2.0 release.
UPDATE: If forgot, one of the problem pages I as using the <a button and the data-role was page. This was very strange but seems to be working now.