KevinTheJedi
Apologies, the header does not match for some reason.
It seems like the first auto-response emails that get sent to the user after a ticket is created don't have their Message_Id's inputted into the thread_entry_email table. But the replies to that email get their Message_ID's recorded, and it works fine afterwards.
Another thing to note is that the headers in the original email and the reply do not match. Neither the original Message_ID nor the reply's In-Reply-To/Reference ID are recorded in the table.
In fact, the table has a bunch of ID's that look similar but I cant find any actual email tied to them.
(I found this out by doing a number of SELECT mid FROM ost_thread_entry_email WHERE mid = "xyz"; queries)
Only the replies' Message_ID are recorded.
But even then, shouldn't the subject line be enough to tack it on as a reply?
I barely touched the template, only moving the ID portion to the beginning of the subject line. 
That is the subject line of the Auto-Response of the ticket created by the reply.

This is the subject line of the Auto-Response of the original ticket where the reply created the ticket above.

This is the reply itself.

That's the template.