I think there is a small bug with Meta-box group extension. The default behaviour on checkboxes inputs is that their label can be clicked to toggle the checkbox. This is assigned by the "for" attribute which should be the same as the input "id".
When a group has a checkbox, after cloning it the checkbox "id" is updated but not the label "for". This means that clicking on the new label will not toggle the new checkbox, and instead toggle the old one (which belongs to the a different group).