I'll start by saying that I experimented a lot before posting. I guarantee that comment-reply.js is properly included, as proof clicking on the 'reply' link moves the form right under the comment I want to answer to.
The problem: when js is on, if I try to reply to a comment, the new comment will still have a comment_parent value of 0, hence making it a new comment and not an answer.
3) Manually changing comment_parent value input trough firebug - if JS is on still no luck.
So basically, when js is on and comment-reply.js is included, I get the nice form moving around thing, but then comment_parent breaks.
Mind this, I checked with web dev tools on chrome and firebug on firefox, the comment_parent input DOES GET UPDATED with the parent it. So you would see that input being updated every time you hit a reply link.
Simply said, on submission, once we reach /wp/wp-comments-post.php $_POST['comment_parent'] has suddenly become a 0.
I logged the whole $_POST many times at the top of the file to know just what comes out of the form. When js is off or comment-reply.js is excluded, all working. When comment-reply.js is running, comment_parent == 0.
Rings any bells? Is this a known issue?
Thanks so much, this took the last 3 hours of my life and I got nowhere yet.