Switching away from Mandrill, I found Amazon SES was sending two emails from my PHP test script. This only happened when hit from the web, running the same script through the PHP-CLI sent one email, as expected.
Looking at Chromes network tab, turns out it was loading the script as well as favicon.ico. Alas, there was no favicon.ico, and in the sites-enabled config for that location the FallbackResource was set to /index.php. Turns out it was loading index.php twice, resulting in two emails.
I used Bradicon! to create a quick favicon, uploaded it, and bam!, just one email from then on.