The MSB definition has some language that allows some common sense in determining who is a money transmitter:
(ii) Facts and circumstances; Limitation. Whether a person ``engages as a business'' in the activities described in paragraph (uu)(5)(i) of this section is a matter of facts and circumstances. Generally, the acceptance and transmission of funds as an integral part of the execution and settlement of a transaction other than the funds transmission itself (for example, in connection with a bona fide sale of securities or other property), will not cause a person to be a money transmitter within the meaning of paragraph (uu)(5)(i) of this section.
Magic City has given you good advice in that you should verify that these are the only financial activities your customer is engaging in. If they are, I think the above language indicates they are not an MSB. The ACH payments they generate are a method executing another transaction, the payment of utility bills. If your examiner's conclusion is correct, virtually any business using ACH would be an MSB...
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In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.