Yeah, the order they appear in isn't the most logical one. I don't know a way to distinguish the newest one with certainty, but a good guess is to take the largest one. (A similar thing happens with any thumbnails one uploads with a set; I have no clue how the one that appears as the main thumbnail is determined.) I've experimented with the system, and here's how to avoid this mess when you are uploading your own files.
Assume you have already uploaded a file and now want to post an update. So you go to the download page of your set and click on 'upload new version'. Then you click the button 'choose file' and search for the new file from your computer. It can be the same name as the older versions, but some choose to change the name to include the version number. It's clearer in a way, but also requires renaming by the downloader if they want their old dac and tws files to work on the new version. Then click 'attach file'. Now you will have at least two files listed above the 'choose file'-button. You can remove the older version by clicking 'delete' next to the file size. This does not delete the whole file, only removes it from the list that is causing the confusion. I think below in the third section, the fields named 'file name' and 'file version' don't actually have anything to do with the real file name, so you can write anything you want in here. That basically means you should take extra care not to write something confusing there, like the wrong file name (particularly if you include the version number in the name), and you should include a logical version number. Once you click 'update submission' you are done. Now when someone goes to download the latest version of your file, the download button on the set's page starts the download immediately, and they don't have to pick from the confusing list. If someone wants to download an earlier version, they are available on the sidebar. If you don't want earlier versions to appear on the sidebar, you have to delete it from there too by the buttons that appear when you hover over the date.
Hopefully that is useful to some, and not too confusing to others.
Assume you have already uploaded a file and now want to post an update. So you go to the download page of your set and click on 'upload new version'. Then you click the button 'choose file' and search for the new file from your computer. It can be the same name as the older versions, but some choose to change the name to include the version number. It's clearer in a way, but also requires renaming by the downloader if they want their old dac and tws files to work on the new version. Then click 'attach file'. Now you will have at least two files listed above the 'choose file'-button. You can remove the older version by clicking 'delete' next to the file size. This does not delete the whole file, only removes it from the list that is causing the confusion. I think below in the third section, the fields named 'file name' and 'file version' don't actually have anything to do with the real file name, so you can write anything you want in here. That basically means you should take extra care not to write something confusing there, like the wrong file name (particularly if you include the version number in the name), and you should include a logical version number. Once you click 'update submission' you are done. Now when someone goes to download the latest version of your file, the download button on the set's page starts the download immediately, and they don't have to pick from the confusing list. If someone wants to download an earlier version, they are available on the sidebar. If you don't want earlier versions to appear on the sidebar, you have to delete it from there too by the buttons that appear when you hover over the date.
Hopefully that is useful to some, and not too confusing to others.