I am having this same problem with my custom post type + custom taxonomy.
For me, selecting a checkbox in the custom taxonomy toggles the Tags metabox, but not the custom taxonomy metabox.
As a toggle, if I select two checkboxes the other metabox returns to is original visibility (i.e. if it starts visible, setting one checkbox will hide it, two will show it, three will hide it again, etc.)
Using ACF PRO 5.2.0 on WordPress 4.1.1.
The two below are not my pics but not sure if deleting them would delete the OP’s pics (?)
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