I managed to get the input out of enigmail and it turns out that the problem
with gpg is only very indirect: The ASCII-armored ciphertext has CR+LF line
endings in gpg4win, while the cygwin version only contains LF. This is probably
the cause of the problem, but certainly not a real bug in gpg4win.

Just to clarify: gpg does not insert just one final line break, it adds a line
break after every line of quoted text. For example,

Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam
nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat,
sed diam voluptua. At vero eos et accusam et justo duo dolores et ea
rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem
ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing
elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna
aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo
dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus
est Lorem ipsum dolor sit amet.

would turn into

Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam

nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat,

sed diam voluptua. At vero eos et accusam et justo duo dolores et ea

rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem

ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing

elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna

aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo

dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus

est Lorem ipsum dolor sit amet.