I have an HDMI auto-switch and the ATV really doesn't play nice with it. I think because it is always on, even when in a low-power mode, some HDMI switches don't recognize it as ever being "off".
Simple solution: put the ATV at the lowest priority input.
Which becomes a problem again as soon as you add a satellite or cable box with the same quirk (as my Verizon FIOS cable box has). Since the TV has 2 HDMI inputs, I put the switch on one with the XBox, BD player, and FIOS on it, and leave the second input for the ATV.