I now believe this has to do w/ the function analyzeSources in \lib\Minify\Minify\Controller\Base.php.
Basically, it goes through all of the files you are minifying and checks the timestamp. If a file has been updated, it then regenerates the minify. Otherwise it doesn’t.
It looks like clearing the cache doesn’t affect minify. The only way I’ve found to update the minify cache is by updating a file referenced to be minified.
Workaround: Add a white space to a file you set to be minified, save, should be good to go.