On a multiple organization appliance, if a user exists on more than one organization with 2FA enabled the token must be reset on each of these organizations in order to be able to see the QR code required for setting up a device for the SMA two-factor-authentication.
If the token is not reset on each of the organizations where the user exists and 2FA is enabled, the user will only see a page prompting for the 'Verification Code' and will be unable to log in to the organization.
This issue has been identified as a defect and will be addressed on a future release.