I installed version 4.3.3 of the plugin and enabled download tracking (by checking "Track outbound clicks & downloads" and specifying "Extensions of files to track as downloads:"), but document downloads are not showing up in Google Analytics.
I am using WordPress version 3.7.1.
I do see Yoast's GA code in the head of the document.
After turning on the Enable Debug Mode, I looked in the web inspector console and did not see any output when clicking on outbound links.
Here's a page with a downloadable document:
Any help would be appreciated.