Sam, I just replicated the issue on my demo instance and the issue is caused by hiding the label.   The variable UI uses the label above checkboxes like a container so if you hide the label then all the checkboxes get hidden as well.   Programmatically it will be difficult to come up with code to dynamically hide the label if none of the checkboxes are checked.   Its definitely possible but would require more time than I have to help in a community setting.

I ended up commenting out the label:

//hideTypes.push("11"); //Label

Then I added 11 to the exclusion list:

if (producerVars.question.type == "11" || producerVars.question.type == "19" || producerVars.question.type == "20") {

      continue;

}

Once I did that the checkboxes showed up and only the ones that I had checked.