I'm having the same issue every once in a while. This is a very volatile bug, its reproduction rate is low, even under the same conditions. Problem is the textarea loads with the style "visibility:hidden", so my guess is the WYSIWYG javascript is messing up (mostlikely by not removing this in all of the cases), but it could be a different number of things.
[image: i.gyazo.com]How I got this. Go to my faction link on sidebar, click on a random person's profile, click on the envelope icon.
User agent string, in case you find it useful: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:40.0) Gecko/20100101 Firefox/40.0
I was just able to reproduce this while having the developer console open on the network tab. As you can see in the screenshot, all the TINYMCE js files are loaded before the loading of messages.php through AJaX. Given the A (to bring down the WYSIWYG editor) doesn't work if the textarea is hidden, I can only assume that TINYMCE is running only once before the loading of the content though AJaX, instead of running again on ajax.success(). This would also explain why sometimes it works, sometimes it doesn't, it depends too much on the loading speed of the message box content.
[image: i.gyazo.com]