Have you created any Drupal "revisions" of your products recently? The updater will only update the current revision of a product.
Can you visit /node/$one_of_those_node_numbers ?
What about /node/$one_of_those_node_numbers/edit ? Does the SKU there exactly match the one in the corresponding error message? Have any leading zeros been dropped?
Please post a few of the actual "Skipping this row." messages.