Upgrade to Custom Press 1.3 problem

Hi Folks,

I have a number of custom post types and custom taxonomies set up through Custom Press. Anytime I try to upgrade Custom Press to 1.3 I lose all of the menus for the custom post types and tax. Further more if I try to visit a one of the tax or post pages on the front end it doesn't exist.

I deactivated most of the other plugins that I thought may be in conflict but still haven't had any luck. I do not use the Custom Fields feature of Custom Press but could it be in conflict with the well-known plugin Advanced Custom Fields?

Any other suggests on how I can upgrade without causing this major conflict?