I have been struggling with this same issue all morning and have solved the issue(I hope I am not posting soon, but so far so good!). I was adding a second content area for a 2 column layout so the client could better understand where the content was going. (Yes, I know you can simply use short code to insert the end and start of new divs.)
Please keep in mind, I use custom field methods similar to this excellent article.
For the post edit textarea displayed value I use:
<textarea class="theEditor" name="content_two_value" id="content_two_value"><?php echo wpautop(get_post_meta($post->ID, 'content_two_value', true)); ?></textarea>
The key is enclosing the echoed value in wpautop().
Be sure to also use the same wpautop() function above for your live display as well.
Many thanks to WPsites as well for the tip on tinymce integration!
Hope this helps someone out!