I have a similar issue with the Prepare screen, but maybe worse. Configurator does not recognize the devices when I plug them in. There is no number at the top on the Prepare icon, and when I click prepare, it says to connect the devices, which are already connected!
I restarted Configurator, restarted the Mac, and wiped the iPads (twice) but still the same issue. Frustrating.
I had a reply to my topic from NYLink with the advice to check the Supervise pane and unsupervise the devices so that you can prepare them again.
What happened in my case was half of my iPads needed a full restore to get iOS7.02 installed - Configurator still had them listed as being supervised, but would not apply any apps to them, and they would not show up in the Prepare pane. So they needed to be unsupervised first before anything else could be done to them.
What I did: I plugged in a single iPad at a time, so that there was no confusion as to which device was which in Configurator - for me, Configurator had decided that all my devices were iPad02. Once the iPad was connected, I was able to go to the Devices menu at the top, and select Unsupervise from the bottom of the menu. After going through one by one, all my devices are now visible from the Prepare pane again, and once prepare was completed they were visible in the Supervise pane again.