Further tracked this problem down to be a gpgtar extraction issue.

Calling gpgtar on the decrypted archive with the same command kleopatra uses:

C:\Users\aheinecke\Desktop>type gpg-archive.tar |"c:\Program
Files\GNU\GnuPG\gpgtar.exe" --openpgp --skip-crypto --set-filename
C:/Users/aheinecke/Desktop/gpg-archive.tar.gpg --decrypt -- -

Produces the corrupted binary. Copying this archive to a GNU/Linux system and
extracting the tarball with GNU Tar produces a valid binary.

Next test on GNU/Linux with:

./gpgtar --version

gpgtar (GnuPG) 2.1.3-beta4

./gpgtar --openpgp --skip-crypto \

--set-filename /home/aheinecke/arbeit/gpg4win/gpg-archive.tar.gpg \
--decrypt -- /home/aheinecke/arbeit/gpg4win/gpg-archive.tar

sha1sum gpg-archive.tar_1_/gpg2.exe

2d387c8fb53d105c31e4cc2ec186e70a365b0c65 gpg-archive.tar_1_/gpg2.exe

tar -fx /home/aheinecke/arbeit/gpg4win/gpg-archive.tar
sha1sum gpg2.exe

54c8c2ec1083943e556255f76ff8f58e623c5b27 gpg2.exe

The second one is correct.

To further minimize the test case:

dd if=/dev/urandom of=testfile count=1024 bs=1024
./gpgtar --encrypt --skip-crypto -- testfile > test.tar
./gpgtar --decrypt --skip-crypto -- test.tar
diff ./test.tar_1_/testfile ./testfile

Binary files ./test.tar_1_/testfile and ./testfile differ

last 512 bytes of testfile are missing after extracting it with gpgtar.

In gpgtar-extract.c extract_regular

  for (n=0; n < hdr->nrecords;)
    {
      err = read_record (stream, record);
      if (err)
        goto leave;
      n++;
      nbytes = (n < hdr->nrecords)? RECORDSIZE : (hdr->size % RECORDSIZE);

^ this does not work for the last header if hdr->size size is a multiple of 512.
In that case the last record will not be written.

Please check my attached patch which fixes the problem.

And the testscript I used to test this.

Pushed your patch to master and 2.0. Thanks.