Update:
Another plugin was adding an order note, which defaulted to customer note:
//$order->add_order_note( ‘Hey, your order is paid! Thank you!’, true );
Solved!
Thank you Maykato. We do not want to disable the email notification, we will use it. We want to disable the default customer note that automates when a customer pays.
We don’t want the system putting in a customer note by itself…
