Correct. The standard WYSIWYG doesn’t appear to have this problem. Here’s an example with the standard WYSIWYG on top and the ACF editor in the History tab below.
Same content in both originally – http://grab.by/JGx6
How content is saved after hitting publish/update – http://grab.by/JGxe
Original with all tags/shortcodes inline – http://grab.by/JGxk
After updating – http://grab.by/JGxs
Original with hard returns – http://grab.by/JGxy
After updating – http://grab.by/JGxA