text: Q:
  
  tick checkbox programmatically
  
  $('#comment-form-subscribe input:checkbox:not(:checked)').prop("checked", true);
  
  If checkboxes are unchecked, manually check them, but this doesn't seem to be working.
  
  A:
  
  You might have a selector issue: I'd check that the length of the jQuery object returned isn't 0. This is what I typically use:
  EDIT: as @nbrooks pointed out, :input is deprecated. This might work:
  $('#comment-form-subscribe').find('[type="checkbox"]').not(':checked').prop("checked", true);
  
  