YES! I have the exact same problem.
I have an older TV that only has DVI input but I've used several other HDMI devices successfully with a simple, passive HDMI->DVI cable, in fact I have two different ones around. I've tried them both, straight into the TV and I get exactly what you describe: wobbly picture, like it's behind a waterfall.
Bad news is, I tried my neighbor's newer Visio TV with HDMI input and it works fine, no waves. So the problem is related to my TV and probably to the HDMI->DVI setup but I'm just guessing there.
I already called Apple support and they were blaming my TV, told me to try making sure my TV was set to accept a 720p signal instead of 1080i but my TV has no such setting (I dug through the manual to make sure). Besides, I've never had to do that in the past. I always send it a 720p signal from my little Acer Revo which has HDMI output via Nvidia ION and it works fine, no changes required on the TV.
So, yeah, definitely a problem here! I'm considering purchasing an HDM to YPbPr converter but they don't come cheap (about as much as the ATV2) and it will probably burn more power than the Apple TV does. GRRRRRR!
Seth