JAL never ceases to amaze me.
For some reason, my or their mistake I don't really know, our corporate TA booked me on JL37 instead of JL35. So the lady at check in was a bit surprised to see me at 10pm. After a bit of me not understanding what she was talking about, the situation dawned on me.
After a bit of back and forth and at least two supervisers stopping by they moved me to the flight I needed, and had intended to book. And even got the "taihen, o matase itashinashita"
I was so bloody appreciative for them saving my bacon, and they apologised for keeping me there so long.
Lesson learned, read mails from corporate TA.