I am having exactly the same issue as described. I’m on WP4.6.1 and have just installed ACF for the first time. I’ve setup a basic image field and then a text field. When I enter text in to the text field and click Publish, the content is updated fine. When I remove all text from the text field and click Publish, the field seems to retain the last value. This only happens when the field is blank.
I do not have WP-Cache as true, I have a very basic install. There are no conflicting field names/ids on the page.
Any idea how I can fix this?