You can't compare 'getent group xxx' with 'groups'.  The first lists
user names, the second group names.

Perhaps you meant to say that 'groups' and 'groups $USER' are not
necessarily the same. The first returns a list that was created at login
time, the second an up-to-date list.  Good to point that out, especially
in connection with my comment #6.

However, the main issue here (bug #1049186) concerns incorrect output
from "getent group", "getent group grpnm" and "groups foo", all of which
(I believe) are supposed to report current information, not information
collected at login time.

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https://bugs.launchpad.net/bugs/1049186

Title:
  sssd forgets group memberships of foo when foo logs in; remembers them
  after ten seconds after restarting sssd

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