We are having the same problem. We upgraded our computer to OS X 10.8.5 and upgraded Apple Configurator to v1.4. We built a new iOS 7 template and created a backup after going through the first run screens. New iPads that are configured from this backup in Configurator still force you to go through the iOS 7 setup screens. We are using a new JSS v8.72 iOS 7 profile. We did not have this problem with Configurator v1.3 and iOS 6. We opened a case with Apple Enterprise support and they are looking into the problem, but no answer yet.

I'm still testing it, but I have had some sporadic luck when I set "Update iOS" to "Never update device"
I will see if I can get to repeat on multiple devices and follow up later.

I think the trick is having "Never update device" set when restoring the backup.

It looks like that only works if the setup assistant was completed and least once before on that device.

Try restarting the device after it has been restored, instead of going through the setup assistant.

You need to do a backup of one that you have gone through the setup assistant and then restore it.