An Apple TV box stopped reacting to the IR when being back in the Apple interface. The light was still changing colors when a button was pressed, but nothing happened. This forum post describes perfectly shows how to get the IR working again. Since it would be a shame if these clear and wonderful instructions would fall prey to data rot here a (slightly amended) copy of them:
1) if you have not already, patchstick the ATV
2) ssh to the atv
(Steps 3 and 4 will fail if you have set the ATV to not auto update its software, since mesu.apple.com will resolve to 127.0.0.1)
3) download the IR firmware update utility: wget http://mesu.apple.com/data/IR/061-3045.20080708.Aq12D/IRReceiverUpdaterTool2
4) download the firmware image: wget http://mesu.apple.com/data/IR/694-5586.20081119.2AvT3/irrxfw-0x0312.irrxfw
(you probably will need to do chmod +x IRReceiverUpdaterTool2)
5) run the firmware patch: ./IRReceiverUpdaterTool2 irrxfw-0x0312.irrxfw
6) if the process worked you should see this message near the end of the output:
Flash Image Verification Succeeded…
SendCmdExitBootLoader
Bootload Success…
At his point the IR indicator blinks yellow. The Apple UI is reacting again. With
an ATV software Version 3.0.2 on a Geforce Go 7300 1GHz ATV the IR became
inoperable after a reboot.
Redoing the update, then unpairing the remote and pairing it again fixed this.
On a side note: I found this blog post 20 minutes after I made it when googling for ‘IRReceiverUpdaterTool2’.
Google is simply amazing.