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 just chose this pdf because it had a variety of controls to test with - this pdf was not created by us. If you fixed this issue for this pdf, is there a chance that it wouldn’t work for actual pdfs that we plan to distribute?
I pushed some changes that seem to make the resulting document work in most viewers (all except the default Chrome viewer for some reason) - let me know if you notice a difference.
If that does not work for you, then as a temporary work around, I find that the set endpoint creates better results, so you could switch to that instead of merge for now - they do the exact same thing and have the same API, so all you need to do it change your endpoint.