Since I am now a consultant - no I do not charge MSBs a separate charge (Hoever, I am available to perform BSA compliance reviews of MSBs
).
However, I have been in banks that do. The important thing would be to insure that your commercial analysis compensates you correctly for checks deposited and cash withdrawn and in addition to that you charge them a separate service fee adequate enough to the cover the cost of on-going reviews and monitoring. I am of the contention that if a bank has a number of MSB accounts, they can pay for the whole compliance function of the bank (and they say that compliance is a cost center - well it is time to turn the tables on that mentality
). I have seen additional fees as high as $1500 for a large MSB.