Have you checked to see that you have made sure that you changed the name clean to cleancopy in the version.php as this is the only folder, in my experience, that can stop it showing up in the theme selector, if not named correctly and in lowercase.
https://github.com/moodle/moodle/blob/MOODLE_33_STABLE/theme/clean/version.php#L35
One other place is in this line:
https://github.com/moodle/moodle/blob/MOODLE_33_STABLE/theme/clean/lib.php#L91
Hope that helps?
Mary