Yes they do, everywhere except for that sub-forum where theme override is on. If I turn off theme override, the flags reappear. If I override with a different theme, the flags disappear. So it's not a behaviour linked to a specific theme.
Member's Country works beautifully in my forum but for one small thing: when I use "Theme Override" to set a special theme for a specific sub-forum, the flags won't show in that sub-forum. Is that a known issue? Cheers.