[Q] rooted S3 can't update official JB

I rooted my Galaxy S3 the other day with the intention of installing one of the JB rom's out there. I thought as my S3 was not locked that the official JB update would be a little way off yet. Yesterday I find the official JB being pushed to my phone. It went through the update process and then said it could not update because my phone had been modified. I checked the rom version and it is now 4.1.1 so it seems to have actually updated everything apart from the interface which is still ICS.

Is there a way to get around this? If I do a factory reset will that wipe the root? Or can I do something to hide the root from the update?

All advice much appreciated.