These sites have rules that don’t allow badges at their live tables. HM2 automatically stops them from showing for you so that you don’t break the terms. Full details of their rule changes are here: http://forums.holdemmanager.com/notecaddy/191131-badges-not-showing-hud-but-replayer.html#post2468872.
The Badges will still show in the HM2 replayer for PokerStars/FTP. They can still be useful for reviewing purposes.
Badges will appear on live tables at other networks which are compatible with HM2 like, iPoker, 888, Party, WPN, Winamax, and others.