Investigating the issue further, we found out that:
If new user is added to a group ID 3 for example, all the other groups that come after ID 4, 5, 6, 7 do not show. But all the groups that come befor: ID 1, 2 show very well.
If user is added to the last group then all the groups that come before show.
That is the issue
The issue seems to be affecting new user accounts after plugin update. Old user accounts do not experience the issue