I’ve tried to do some digging around in the code. Without setting up a ajax loading acf form myself I can’t really find a solution.
I believe that inserting a WYSIWYG field causes ACF to enqueue scripts that load into the footer of the page that format the field and since you’re loading the form by ajax these scripts are missing.
Look at the footer script on a page with a form loaded normally and on a page with a form loaded by AJAX and see if there is a difference. If there is then you’ll need to figure out how to load the scripts that are missing.
Not sure if this will help but I found it after writing the above. Have you looked at this http://www.advancedcustomfields.com/resources/acf_form/#AJAX
