Some of these background were so obviously strong for some character class that in a living campaign we could end up having 80% of characters coming from the same background.
For example, Orb wizard and the Thay background... We are talking a 6 to (in extreme case) 12 hp difference. Not a lot of Living
FR orb wizard would come from elswhere!
Impiltur would probably do the same for Avengers.
Other backgrounds are just flat out stronger than their general counterpart.
Consider Cormyr :
Insight becomes a class skill AND you gain +2 to Insight AND you gain +2 to saving against fear effect. Any of these three elements could be considered a sufficient background benefits...
So yeah, ban then, ban them hard!