Why did MarketPress stop linking to all categories and cart pages?

Built WordPress site in a sub domain of our URL to test and develop. Installed MarketPress and tested features, installed products. Everything seemed to work except the Authorize.net function. When We went to "check-out" a Page not found error occurred.

Assumed it was the sub-domain issue.

Had host move all files and database to top level. Now all MarketPress functions and pages are inaccessible except through the dashboard.

Help.