It doesn't really matter what's the type of object they originally were. The form detection wizard works on a visual basis, not based on objects. Basically there's nothing much you can do about it, except try to find an object that is recognized as a check-box.
Another option is to use a script after running the wizard to convert those files to check-boxes.
Or you can use OpenOffice, which can generate PDF files and convert the fields in the document directly to the same kind of fields in the PDF version.