Consumer requests a stop payment on a pre-authorized, non-recurring ACH item. Upon proper notification we place a 30 stop payment on these items. The stop payment will fall off on the 31st day. Our auditor is telling us we may be in violation if the item in question was to be presented for payment on the 30th day which happened to be on a non-banking day or holiday.

Is the thirty (30) day time period correct in this situation?

per NACHA operating rules (page 0R46, subsection 3.7.1.4 effective period of stop payment orders):

a stop payment order will remain in effect until the earlier of:

a) the withdrawal of the stop payment order by the receiver; or

b) the return of the debit entry, or where the stop payment order applies to more than one debit entry relating to a specific authorization involving a specific originator, the return of all such debit entries.

so, if it makes you feel any better, you are both incorrect

It's implicit in HG's intentional failure to mention Reg E that this stop isn't one that Reg E requires you to accept, but NACHA rules do.