Thank you Jonathan for your investigation. I was going to try your filter code, but after updating WordPress to 4.3 the problem is gone!
I tested on two installations and saw the same thing on both. After updating WordPress to 4.3 the scrolling and fixed size of multiple ACF wysiwyg editors is back.
(Before updating to WordPress I also updated ACF to 4.4.3 so it could be a combination of WP 4.3 and ACF 4.4.3, but only updating ACF did not change anything.)
I’m going to mark this answer as “This solved my question” but I’m still thankful for your previous answers.
