Quoting from this docs http://docs.moodle.org/dev/lib/formslib.php_Form_Definition#checkbox :-
BEWARE: Unchecked checkboxes return nothing at all (as if they didn't exist). This can surprise the unwary. You may wish to use advcheckbox instead, which does return a value when not checked. 'Advcheckbox' eliminates this problem.
This led to the issue
I am creating this issue to make a review of all 'checkbox' usage and make sure it is not happening anywhere else.