I'm new to ATV Flash, but I'm pretty experienced with AppleTV, Mac's, WMV files, Flip4Mac, etc. I'm finding that if the AC3 pass-thru option is enabled, and I'm trying to play a .WMV movie, thre is no audio. Other formats like .MP4 work flawlessly.
The latest updates of Perian, MPLayer, Flip4Mac, etc. have all been applied.
Thus far, this is the only bug I've seen.