Another WP eCommerce issue with Atahualpa...ideas welcome!

Upgrading to all current versions of theme and WP e-Commerce plugin. Products are not updating in regards to permalinks which is breaking the search functionality. Products page loses the right sidebar and overflows into the footer. This seems to mean that the plugin has not synced with Atahaulpa theme settings as it is supposed to. Before posting here, I have tried all of the suggestions for upgrade including following step by step after watching the WP e-Commerce video for this created by one of thier experts. Tried using an older version and it broke my admin panel preventing access to any of the products for editing. Also, did try turning all plugins off and changed to TwentyTen theme as suggested. All but the product search being completely correct worked fine but upon returning to my theme of choice for this site, Atahaulpa, the errors reappeared.
This is the site: www.doorstepdelivers.com
Any ideas or fixes will be much appreciated. ~Inblingham