I'm using Ubuntu 16.04. When I use LightDM to login and start X, I see that my secondary groups aren't loaded (running "groups" reports that I belong only to my primary group). If I log in via console or if I su in a term in X, the groups command works normally, reporting my primary and all of my secondary groups.
Curiously, even though "groups" does not report that I'm a member of sudoers, I can still sudo. Similarly, I can run mythfrontend, even though I'm not reportedly a member of mythtv. It seems as if the OS recognizes my secondary groups, even if the groups command does not.
So, it doesn't seem to cause a real problem, but I'm curious if anyone else has seen this behavior. I have three other machines running Ubuntu 16.04, but groups works normally on each of them.