Hi Hayden,
You haven't mentioned what you have in your environment for Control Centers... The Control Center provides the Central Management of the Scanners, so when you say you origninally had 1 Scanner, was this appliance actually performing both the Scanner and Control Center role? And did you maybe set up the new appliance as a Scanner and Control Center as well? What you would have wanted to do was configure the second scanner as a Scanner only appliance and then add this Scanner to your original Control Center/Scanner. Make sense?? This is if I've guessed correctly, but we'll really need more details here, product, version, build number, roles of the appliances...
Kevin