Configurator won't check in devices ("Device running newer version")

We deployed ~400 iPads using Configurator in August. When iOS6 was released, students received pop up notices that they needed to upgrade their software (not to mention they knew that Siri was being added) so about 1/2 of them upgraded their iOS. Now, if I try to check them into the configurator so that I can refresh their iPads, I get the "Device running newer version" error message. Any ideas?

I have the responsibility in our school district for developing and testing user procedures for managing iPads in the schools using Configurator. We have 600 iPads being managed by Configurator on 16 sites.
We cannot find a way of restricting users (students or teachers) from updating the iOS while using the iPad. Any mis-match of iOS version means most Configurator functionality will no longer work. Refreshing a backup, installing a new profile, and using the Assign Checkin/Checkout ALL require iOS congruence. This occurs not just with major version changes, but also with the near-weekly iOS patches within a version. "Device running newer version" errors occur with a mismatch between 6.1.2 and 6.1.3.
This causes a lot of frustration and overhead in maintaining a standard image on the iPads. At worst, students lose their work if they cant check the device back in.
Ideally, we would like to control the timing of version updates. Is there a prescribed way to do this?

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Your MacBook Pro can be updated to run Mac OS X "Snow Leopard". Buy it. That will enable you to run the latest iTunes version.
Online (US): http://store.apple.com/us/product/MC573/mac-os-x-106-snow-leopard
Online (UK): http://store.apple.com/uk/product/MC573/mac-os-x-106-snow-leopard
Germany: http://store.apple.com/de/product/MC573/mac-os-x-106-snow-leopard
Elsewhere: call the phone number in the Apple Online Store
Apple's price is $19.99, £14.00, €18.

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Configurator won't check in devices ("Device running newer version")

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