Answer: Your payer was probably denying these claims because you may only report multiple motion analysis test sessions — not the number of conditions under which the podiatrist ran the test. This means that the same code counts for one session, regardless of how many trials the podiatrist ran.
In the example you gave about the patient retested with and without her orthoses, you may report 96002 (Dynamic surface electromyography, during walking or other functional activities, 1-12 muscles) only once.
However, this doesn’t mean the patient has to have a completely separate appointment in order for you to report a motion analysis code twice. Here’s an example in which a patient has two different sessions in one visit:
A patient undergoes two fine wire electromyographies. The first test monitors the flexor hallucis brevis muscle, and the second test monitors the abductor hallucis muscle. In this case you may report 96003 (Dynamic fine wire electromyography, during walking or other functional activities, 1 muscle) twice.
However, if the podiatrist ran one test on the flexor hallucis brevis muscle and two tests on the abductor hallucis muscle, you may not report 96003 three times.