I have just downloaded the Popover plugin and opened the zip file, it contains:
I have tried placing the file(s)/folder in both(Not simultaneously) wp-content/plugins and wp-content/mu-plugins/ with and without testheadfooter.php.
The result on all counts was that the plugin installed, but when I tried to use it I couldn't drop rules onto the page.
Also the testheadfooter.php file installed it own plugin!!!
I have attached a screenshot.
Everything installed on the site so far is the latest version and I removed the five non WPMUdev plugins to test (41 plugins total). WordPress 3,1
The site is/will be a MU instance.