When flattening the form, all form-fields are put at the bottom of the file, overlapping eachother.
When I just look at the file however, without flattening, everything seems to be ok.
Workarounds so far is to reset all BBox-es for PDFormXObjects to start rendering at (0, 0) before we flatten the file.
We've also tried setting the form-fields to 'read-only', which also visually left the PDF in tact but is not a real substitute for flattening.
Attached are a PDF with the issue present and the OpenOffice-Drawing that was used to create the PDF