I found a bug while using a custom taxonomy and having the ACF plugin turned on. When selecting a taxonomy term in a post the custom taxonomy meta box hides itself. I can turn it back under “Screen Options” but then if I want to change the taxonomy term again, the meta box will hide itself again. When I turn of the ACF plugin it works normal.
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 (?)
I opened a support ticket with ACF and am still awaiting a reply. If I hear anything on this topic I will be sure to share. I am experiencing the same issue that when I check a box for a taxonomy my entire meta box disappears. I noticed that somehow the JS is adding a hide class to the meta box after the taxonomy selection.