I have the same problems from October, updating WordPress and Bbpress in this months doesn’t take any difference. I did a similar solution as pointed above from “Ronthai”, I’ve disabled the “Setting->Forum->Reply Threading” check. The order come back normal but you don’t have nested reply. My solution (as some post above) was to install this small plug-in to add a Quote link: https://wordpress.org/plugins/bbpress-direct-quotes/
I write down my setting for debug propose:
Wordpress: 3.8 (bug present also on 3.7)
Bbpress: 2.5.3 (bug present also on previous version)
Template: NewsPlus
Apache version 2.2.23
PHP version 5.2.17
MySQL version 5.5.34-MariaDB
Architecture x86_64
Operating system linux
