After upgrading to ACF 4.0 today we received several reports of folks not seeing the custom field meta boxes when editing pages, etc. We narrowed it down to folks using IE9 with Compatibility View turned on. When CV is turned off, the plugin functions properly. And we confirmed that this definitely wasn't an issue with the prior version running on our sandbox site. Unfortunately I could not nail down exactly what was failing, but I did notice that in the Screen Options drawer, there were additional checkboxes up there that didn't apply to the page in question (like custom field meta boxes that were template-specific but not for the current template). Perhaps you could look into it?