I'll add my voice to the list, as I'm having similar issues. First my set-up:
iMac - a bit long in the tooth (and hopefully being updated after WWDC!!), OS 10.7.4
2 x AppleTV (3rd gen), software 5.0.1 (4224)
Time Capsule, software 7.6.1
iTunes 10.6.1 (7), library file on iMac in usual home directory location, media all on RAID HDD, connected to iMac via FireWire (it was originally connected to the Time Capsule via USB, but this was getting complicated and the iMac is never switched off) ~ 1 Tb music, movies and TV shows
I also have an iPhone, iPad and MacBook Air - but not really used in this setup
Connections:
iMac to TC via Ethernet
TC to AppleTV number 1 via Ethernet and to number 2 via WiFi
And now the issue:
Generally works well
Occasionally requires me to restart iTunes in order to see my shared library on either AppleTV, generally works OK
After watching a show OFTEN requires restart of iTunes to access library and select next show
Normally playback is great, once running. Occasionally playback is very stuttering, until I restart iTunes
The same media is accessed visa Sonos system, with no problems whatsoever. Even if the computer is asleep.
The whole setup is quite new, so I can't say if it is related to software versions. The external HDD seems to switch on OK, the light goes on and I can hear it spin up. Waking the computer manually from sleep doesn't seem to help. Restarting the AppleTVs doesn't seem to help either. I have no idea about IP6 settings, but surely these shouldn't need to be altered, given that this is Apple's consumer oriented end of things!
I, like others, will await a solution