Categories and Side Bars Don’t Function After Migrating from Media Temple

Hello, we migrated our website from Media Temple to Wordpress.com Pro account. In the Migration, using All-in-One WP Migration, the Categories no longer function. I have the categories we can see that they are set up correctly, but when we go to the pages that the categories used to show on they no longer show. I asked WP to help and they believe that it might be a theme issue. Have you seen this problem before and if so what do you suggest?