This bug has to do with the frag deflator thread in mksquashfs. I
haven't fully determined the problem but it is likely due to parallel
processing (NOTE: the '-processors 1' option does not solve the bug).
There's an out-of-tree patch that disables the thread by removing its
working queue:

  https://github.com/intrigeri/squashfs-
tools/commit/c2c4d15580adee66b68c29eb9d2ee660225449bc

I've verified that the patch results in consistent, reproducible
squashfs images:

$ md5sum *.snap
0161f2c324cb2753429b8c51818132c5  nmap_1.snap
0161f2c324cb2753429b8c51818132c5  nmap_2.snap
0161f2c324cb2753429b8c51818132c5  nmap_3.snap
0161f2c324cb2753429b8c51818132c5  nmap_4.snap
0161f2c324cb2753429b8c51818132c5  nmap_5.snap
5fccb0276e2cd329021591129855eb83  nmap_7.12SVN-0.4_armhf.snap

Note that nmap_7.12SVN-0.4_armhf.snap is the snap that was originally
attached to this bug which was created with a mksquashfs that had the
frag deflator thread enabled, so its snap differs from the ones created
with the patched mksquashfs.

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https://bugs.launchpad.net/bugs/1576763

Title:
  pi2 images generate different checksums on repeated runs

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