I think you have a problem with Taxonomy check box, it just save the new checked items
i mean when you choose to remove the checked from any previous selected term within the filed "checkbox" [ Populate with a Taxonomy by gravity form custom post types plugin] the taxonomy field doesn't save the unchecked items.
and it appears in the admin area that the user still select this term and didn't unselected it.
Wordpress V. 3.4.2
Gravity Forms + Custom Post Types Version 3.0.1
Gravity Forms - Update Post Version 0.5.3
Thank you in advance