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Can you tell us what problems or errors you are running into when trying to upgrade to iOS 6? Yes, you can't upgrade a jail broken iPad using the over-the-air (OTA) function, but upgrading to the most current iOS is always an option. So, please, give us the details of you issue and I am sure we can help.
Do note, however, that there is no jail break for iOS 6, yet, so you'll have a stock iPad when you do go to that firmware...
Marilyn