Hi Brainer,
Which basic/regular badges are you referring to? You said the basic 5 badges work, right?
You're saying that the Holdem badges were working for Holdem, right? Which is good.. They have opposite badges too, are you sure it wasn't an opposite badge showing for your example who always donk-3bet?
Your NCE Holdem package shouldn't interfere when you're playing Omaha, and the Holdem Badges should not appear there.
After you've reset your notes, do you experience the Holdem badges working well for Holdem? and only the default badges (which are applicable to either game type) showing for both Holdem and PLO? That is what you should have I believe