There aren't different categories for the old puzzle and the new. The old puzzle shaves off around a minute. Is there any plan to make new categories for this or do we just upload runs competing against that time.

As far as i'm aware, it's just trying to compete with the old time. This should be discussed by a moderator tho, splitting the runs is not a bad idea.

typically if a new run is submitted from a current version any older runs on previous versions are considered out of date and removed.... sub categories usually take time for that to be seen because they aren't run as often as main branch

(you still need to remove the old chapter 1 runs <3)