@Elliot Condon I think this is related to:
http://support.advancedcustomfields.com/forums/topic/new-version-not-showing-fields/
http://support.advancedcustomfields.com/forums/topic/custom-fields-disappear/
I am also experiencing this bug, there is something wrong with the Location Rules and Screen Options. My ACF meta boxes are hidden by default when I use location rules. I am using page templates as a location rule. Using WP 4.1.1 and ACF Pro 5.2.0
