Well, it turns out the majority of the reputation issues that we’re seeing is more of a display issue. So I don’t know if what they are seeing is the same thing. We have a Support Article up that mentions it.
The War Within Prepatch: we are aware of a display issue where characters can earn large amount of reputation followed by a decrease as an adjustment. The total amount of reputation earned is correct.
Basically what is happening is the client as if you gained it from zero. So say you have 1000 reputation already from your Warband and your character gains 100. The display shows that you received 1100, then the system catches up and corrects for the original 1000, showing your reputation has decreased. The final value should otherwise be correct. It’s something we hope to have fixed in a future patch.
In the meantime, you should be able to prevent the weird calculation from appearing by talking to a NPC of that faction to populate the reputation preemptively in your list.
That would be my question because it seems like you are exalted with those reputations but you are into the paragon rank.