Are you setting the sort order for the Versions in the playlist?
The easiest way, I find, is to set the order using the playlist view in the Media app in Shotgun.
In addition to drag/drop that the media app provides, it also has a
Save Current Sort as Sort Order. Once you set up your sort as you like it, choose that option and it will populate each version in the playlist with a sort order.
Don’t worry though, that sort order is specific to the Version+Playlist, so it will only affect the sort order for the versions for the current playlist.