I have recently been having the same problem with enigmail as this user:
https://sourceforge.net/p/enigmail/forum/support/thread/de00ae35/
Quoting him:
"If someone sends me an email encrypted and signed, I received it correctly. If
I do a reply, encrypted and signed, of that email, the recipient will receive
the reply wit additional blank lines after each original message line."
However, this is not a problem with Enigmail or Thunderbird: I began
experiencing this issue after switching from the Cygwin GPG executable to Gpg4win.
I can reproduce the problem locally and after switching back to the Cygwin
executable, the problem does not occur.
Ways to reproduce:
Write a text-only message to yourself, longer than one line, encrypted with
enigmail.
When you receive the message, hit reply, type something under the quote and send
it, encrypted.
As soon as you receive this (second) message, there will be additional line
breaks in the quoted text that don't belong there.
If you change the GPG executable in the Enigmail settings to gpg.exe from the
bin directory of a Cygwin install, this does not happen.
Unfortunately, Cygwin GPG is an old version and Enigmail warns me that they will
stop supporting this version soon. It would be very nice if gpg4win would behave
like the gpg.exe from Cygwin in this context, because it makes longer email
threads practically unreadable.