No Javascript Download Confirmation when there should be

This is with the free version.
Problem: When any user clicks on a download link, they are not getting a confirmation letting them know how many downloads they have left. Quote—

“the system will politely ask the user to confirm the download using a very intuitive JavaScript confirmation prompt, which contains specific details about your configured download limitations…”

This isn’t happening.

Now the scenario I have is complicated so before people start talking about disabling plugins and going to default themes let me present the actual file download system setup.
We have over 600 files available to download and we add 4 almost every week. Each file is audio and has a description, title etc. To manually input these onto a single page for access would be very time consuming. So I created a php script that can read a directory inside the s2member protected files area and spit out a list of those files. In order to cut back on server load I created multiple sub-directories. So s2member-files/600-699/filex.mp3 would be your basic link. To make sure it wasn’t my script causing an issue I put a raw link on a page using this format.
<a href="https://domain.com/?s2member_file_download=/600-699/filex.mp3">Download</a>
clicking on the link does actually trigger a download but not the confirmation dialog. Why would this be happening and is there a way to force a confirmation. I know there is a way to suppress them.

Are you sure you haven’t done that at some time previously? If not, you need to check for javascript errors. Press F12 and click on Console. Then, if necessary, reload the page. Do you see any errors?