Could you check in phpMyAdmin that all of your Products have master_categories_id values ...

Also have you applied all of the Known Bug Fixes:
http://www.zen-cart.com/forum/showthread.php?t=82619

NOTE: this is also a good time to check that you have applied all of the Security Patches and Updates:
http://www.zen-cart.com/forum/showthread.php?t=131115