If you have progressive profiling enabled on a form and have checkboxes on that form and have checkboxes that are defaulted to "checked", then these checkboxes will disappear if the page is visited twice (or if the page is refreshed) by the same user, but never submitted.
Marketo support claim that this is by design (support case # 129497), but to me this is very much a bug and needs to be fixed.
My logic:
If a user has never submitted the values, they have never given the signal that the values are correct or accepted by them. If these checkboxes are indicating "opt-in" acceptance, for example, they need to stay visible until a submit action has taken place.
The fact that they will be hidden before a submit seems to say that just viewing them once is the equivalent of submitting them. I totally disagree with this logic and I do not see any other fields that behave this way.
My conclusion is that there's a bug with the checkbox field's progressive profiling logic. I'd like to see this fixed.