I have a very similar issue — just slightly different. I have a custom taxonomy metabox and the normal Categories metabox showing. As soon as I click on any given taxonomy term or category, the Categories metabox is instantly hidden.
I can get it back under Screen Options, but it goes away again if I click any term again.
WP 4.1.1 & ACF 5.2.0, and as above, when disabled, the problem goes away.
