I just re-tested on default WordPress and it’s working normally. I also use the plugin on several of my own sites, and they all are working fine. Plus there would be a ton of support tickets if the plugin suddenly stopped counting downloads. So the issue most likely is specific to your setup, site, server, or something.
So continuing with troubleshooting, on your test site (default WP setup), try switching to one of the default WordPress themes (while all other plugins are disabled) and try again. There may be something in your theme functions that is causing an issue with downloads.