Just figured out it was being eaten by AppArmor.
For anyone else, you need to add:
#include <abstractions/authentication>
to /etc/apparmor.d/local/usr.sbin.squid
and reload apparmor
** Changed in: squid (Ubuntu)
Status: New => Invalid
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https://bugs.launchpad.net/bugs/1608984
Title:
PAM auth no longer works after upgrade to 16.04.1
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