I was hitting the back button to retest to show the inconsistent results, but also refreshed the page so you'll notice the checkboxes clear out each time. I've also tried this using the disabled cache setting in Chrome developer tools. From doing some more research it appears the following function within post-functions.php is not recognizing a payment value consistently. Here is the function that is supposed to recognize a value for Stripe.
//return true if a payment-enabled form is being submitted and has value (not zero)
//currently this is only being used for stripe, authorize.net, braintree and paypal pro
function mf_is_payment_has_value($dbh,$form_id,$entry_id){