I'm having the same problem as the one described in this post:
https://gvectors.com/forum/general-questions/secondary-usergroup-options-missing/
I have 2 Usergroups that can be marked as Secondary (1 Registered and 9 USA - Denver, CO):
But only one of them appears on the Account page for a user:
I am using the User Custom Fields addon. Does it have something to do with the value that is listed in this field?