My wife's company also has a deal with a 'major' agency. The have a long list of charges that apply. Since the airlines no-longer pay commission they charge for just about everything. A fee for booking, fee for ticket issuance, a fee for 'printing' ( attaching to an e-mail) an itinerary, fees for hotels, fees for ground transport, fees to scratch their bums. etc.
I'm sure that airline booking/card fees are not absorbed by the agency but who knows. They make considerably more per booking than the days of a 9% commission.