I have never been asked to take my Kindle out. The only time my Kindle was specifically inspected was flying home from New Zealand shortly after the underwear bomber stunt. There was a secondary security screening that required that every person on the plane was pat down and all carry on luggage was hand inspected.
I would remind you to turn off any WiFi or 3G connection and put your Kindle in sleep mode before sending it through the machine. There have been a few reports of people having problems with their Kindles not working after going through the machine and pretty much all of those people reported having left their WiFi or 3G on.
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