A Purrs member called Sheila went ahead with the Sureflap upgrade and so far as I can recall, she had no difficulty with it.
We've got two Sureflaps one of the pet door types and one of the new dual scanner types. We've found Sureflap to be very helpful, so hopefully they'll be able to give you some assistance, as I think you've taken most of the steps we would normally suggest, such as making sure the door is clean so the scanner can read the chips, and checking the batteries. If it isn't even allowing you to set it up, I would try a different set of batteries, just in case - I have known some to be duds before they've officially expired.
In the meantime, welcome to the forum, and tell us about your new kitties
What are their names, how long have you had them and what are their characters like?