All the Moodle instances were using different configs. I discovered the problem by running php admin/tool/phpunit/cli/util.php --install and was able to see the initialization process was being killed because php was out of memory. After allocating more memory to my VM, I am finally able to run the phpunit tests on the 3.6 installation now!
Thank you for your feedback - the help is most appreciated!
Thank you for your feedback - the help is most appreciated!