Well, I’m not really the plugin author. I’m just a user like yourself. I just happen to answer a lot of questions here.
In this case, if you haven’t already done so, the best chance you have of getting someone to help you with your specific problem would be to submit a ticket here: http://support.advancedcustomfields.com/new-ticket/. The people that take care of those tickets can do a bit more that those of use just answering questions.
Just saying though, ACF only uses standart WP WYSISWG editors, so the theme really is doing something wrong if it messes those up.
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