I was originally looking to reply to this post as it went unanswered but closed anyway: https://www.ads-software.com/support/topic/paragraphs-removed-from-new-posts-in-update-39?replies=20
Anyway, after upgrading a client website to the latest WordPress (3.9.1), we also discovered this big issue, basically breaking formatting on all new content published/edited due to a lack of paragraph tags in the WYSIWYG (newlines no longer create p tags).
To fix this, in your functions.php file (https://codex.www.ads-software.com/Functions_File_Explained), put the following (or similar if you have this filter already):
function themename_formatTinyMCE($in)
{
$in['wpautop']=false;
return $in;
}
add_filter('tiny_mce_before_init', ' themename_formatTinyMCE' );
Obviously change ‘themename’ to anything you want ??
There seems to be hardly any help with this anywhere else, so I hope this helps!