I was given a pointer to the Ubuntu Policy Manual, in section 9.3.2 it
says

"In Ubuntu, /var/run is mounted as a temporary filesystem, so the init.d
scripts must handle this correctly. This will typically amount to
creating any required subdirectories of /var/run dynamically when the
init.d script is run, rather than including them in the package and
relying on dpkg to create them."

which is why I suggest in the bug report that /var/run/sks be created in
the init.d script - which is indeed what I have done as a fix for this
bug.

-- 
/var/run/sks not presistent across reboot
https://bugs.launchpad.net/bugs/313684
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