30 Day Waiting/Vetting Period Prior to Granting OD

My bank has a 30 day waiting and vetting period prior to us granting overdraft service. We do not have overdraft services that come with the account but rather it is our practice to offer an OPT-IN to Standard (payment of checks, ACH.) and then we offer another opt-in to Extended Service which allows the payment of ATM and one-time POS into overdraft under Regulation E. In this example, the customer opted in to both Standard and Extended Service. Customer received the Regulation E confirmation notice. Without waiting the 30 days initially disclosed, my bank immediately paid into overdraft ATM and Debit card charges and fees but returned the checks that came through as insufficient. Once the 30 day vetting period for this customer had expired, they denied the customer for overdraft service but continued to allow only Extended service, ATM and One-time debit payments and charges to go through. It is my understanding that the Extended Service under Regulation E is pursuant to the overdraft program offering and not to be used as a stand alone service outside the overdraft program. If we rejected the customer for our overdraft service, shouldn't that include all transactions?