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Wish I could help you. I read the thread title and thought I had the same issue, but mine is different. Mine is more of a true stutter, no freeze, and my media is on the ATV hard drive. Any idea of what is going on there? The pictures scrolling on my screen saver every once in a while 'flick/stutter,' and then start moving again. Same w/ the music. It'll be like a needle skips for just a second (note: Those born in the 80's and after, a needle is what we used to play 'records,' a primitive form of music listening).
 
If a reboot of ATV and reloading iTunes doesn't work, I find the best thing to do is leave it alone for a while and go do something else, then come back and try it.

I'm not sure why/how/what, but when this happens, I get the idea that ATV itself is doing "something" which is hogging its resources or thrashing its HDD, but 5 minutes, 15 minutes or 30 minutes later, its done whatever its doing and works fine.
 
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