Consulting the PDF Reference (looking at version 1.6, available at
http://partners.adobe.com/public/developer/en/pdf/PDFReference16.pdf ),
it seems that the problem is that the FDF being generated is incomplete.

While the spec requires the FT (field type) key only in the PDF itself
(p. 637), it doesn't include that key in the FDF format (p. 677). (This
is why I'm guessing as to which fields are button-type and which are
text-type. It might be helpful, though, to include a comment above
non-"Tx"-type fields--that is, "Btn", "Ch" or "Sig"--which would help
the user to interpret the value. (Radio buttons and checkboxes are "Btn"
fields, the specifics of which depend on the value in the Ff key, which
(I think) is allowed but not required to be exported.) The V (value) key
for "Btn" fields is "a name object representing the check box’s
appearance state, which is used to select the appropriate appearance
from the appearance dictionary" (p. 648); I don't know how much other
stuff that pulls into the FDF file--maybe it just references a
dictionary kept in the PDF itself? It looks like the names are
predefined ("appearance for the off state is optional but, if present,
must be stored in the appearance dictionary under the name Off. The
recommended (but not required) name for the on state is Yes") but the
name for the "on" value can be changed.

In any case, it appears that the value for the checkbox fields, if not
the radio fields, should read "/V /Yes" or "/V /Off", which suggests
that most probably the field values aren't being properly exported--
that, or (somewhat less likely) there's something fishy with the test
PDF itself which causes the button fields not to export properly.

-- 
generate_fdf followed by fill_form changes checkbox fields
https://bugs.launchpad.net/bugs/192410
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