That doesn't sound right. If they allow a DC to bill for the ultrasound and electric stim they should allow the manipulation. It sounds more like you are just not billing the 98940 or 98941 the way they want it. For example, they may require a modifier, or maybe they don't all the manipulation (98940-98942) codes. I would contact the provider rep for your area and ask them to first check to see if the patient's coverage allows chiropractic benefits and if so, what codes do they allow them to bill for and what are the rules regarding the billing.
Michele