Tokenization with multiple merchant IDs

We tokenized in December (with Vantiv) and we are now running into some problems. Credit cards that were tokenized by the utility are being declined during online purchases. It appears that having separate merchant IDs for retail, MOTO, and eCommerice may be causing the problem. But we may not have set up our payment method groups correctly before tokenizing. Has anyone else run into issues and how have you resolved it? I would love to hear from other orgs that have successfully tokenized with Vantiv who also have more than one merchant ID account.