This is an easy problem to fix: the members of those user groups will need to go into their profile and select their status flag before the flag will be visible to other users.

This setting is located in their Public Profile section. If they are able to have status flags, they will see a drop down menu next to the Status Flags option. (This will give them the choice of displaying their flag or 'None', to not display it.)

Once they've made their selection, they will need to click the Proceed button to confirm their choice.