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Are you referring to the checkboxes that are supposed to appear when you select a "Delivery Method"? It looks the checkboxes are hidden based on CSS whose selectors start with "et". So I'm guessing your theme is the culprit.
It also might have to do with something that got changed in the formidable styles for checkboxes. I'm seeing some questionable stuff in:
.with_frm_style .frm_checkbox input[type=checkbox]
I can see your checkboxes but you have quite a few jQuery errors on your site. That's a problem.
I didn't see any jQuery errors until I cleared my browser cache and then refreshed the page (which looks completely different now). I'm guessing you disabled the theme? Off to continue cooking dinner...