We are still investigating exactly what is going on here. What seems to be happening is that certain PDF viewers do not like the way we are setting the checkboxes (even though we are following PDF Spec).
This is actually somewhat common as every PDF viewer implements the PDF specification differently, and many times certain viewers will not fully implement the spec which leads to scenarios like this.
Technically this is not an issue on our end as we are following the PDF spec, however we will continue to investigate and see what we can do to make the checkboxes appear as expected on all PDF viewers.
In the meantime, it would be useful if you could send us the PDF you are testing with, and also let us know which viewer you are opening the downloaded document in.
I will reply here with any future updates.
Thank you for your patience!