I have filed a report about this problem in the Samba 4 BTS.
https://bugzilla.samba.org/show_bug.cgi?id=9237
** Bug watch added: Samba Bugzilla #9237
https://bugzilla.samba.org/show_bug.cgi?id=9237
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https://bugs.launchpad.net/bugs/1049186
Title:
sssd sometimes forgets all but one group memberships of a user
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