With the falsification of business records, the situation does not seem as clear-cut. It is wrong because it is preventing the public or other relevant parties from having access to accurate information. I don't know if one can really make a formula to calculate how much damage is done by a given falsification, but I personally do not think I would include the number of checks or (probably) the number of invoices written in that formula. The method of payment seems mostly incidental and not essential to the wrongness of the crime. (I include the number of payments as part of the method of payment.)
If this does not clear up my position, feel free to let me know. There is more I could write to flesh it out, but I don't know if that's necessary or if it'd be overkill =)