If the player character sides with Seagrave Holmes during the Council Seat quest, the prices of the items bought at the store are risen by the same amount they are lowered at Holmes' store.
Bannon will speak normally to you, even if you sided with Holmes. He will reply with the usual "I think I've seen you in here before" when asked about trading. However, once you say you are here to trade, he will reply with "If I must".
Sometimes when speaking with Bannon the Council Seat quest may glitch making it impossible to complete as the proper dialogue options will never show up.