Have a similar problem (recently the audio does not come at all, needs to send any video source first or switch to different speakers several times to get it working), plus when using the remote app from my iPad2 or iPhone the track "time clock" don't sync sometimes, also several audio flicks when the TV is off or on, once I don't feel like I need the receiver audio when watching TV Shows and related, the HDMi goes straight to the TV, the optical stay on the receiver.
Before I had an Airport express in the same place, but I never had any audio problem with it, for some reason I feel like the audio quality of the ATV is poor when compared with the Airport express when playing CD's encoded in Apple lossless format.
Stuffs in this setup:
-time Capsule (main router)100/1000T 32 ports Netgear splitter on it.
-airport express (in the kitchen working well also connected via optical audio on a very old Onkyo receiver used for audio and stereo only).
-Airport Express first generation (In bath roon, analogue connected working well, wireless off)
-apple Tv 1 in the bed room (working well also via optical audio on a old Yamaha's receiver)
-First generation MacMini (no monitor connected)just used as Home Music server, controlled most of time via remote app, & remote desktop from the other macs in the house using home sharing to transfer the files.
-Apple Tv 2 in the living room, connected on a Denon's AVC-A1HD receiver via optical cable, and via HDMI straight to a Sony Bravia TV. No HDMI pass tru supported for the ATV due to the BD recorder set up and Japanese copy laws.
All the devices in this list is wired with CAT 6 Lan cables, also all checked recently.
Got the ATV2 6 months ago the software is up to date, but the problems is getting worst over the time, (too much audio Flicks) should I send it to repair? Any suggestion are welcone, Thanks.