Here's what I have done:
- Ripped a Blu-ray movie to an MKV
- Used Handbrake to transform the MKV to MP4
- Added the MP4 movie to iTunes, and also copied the file to a USB thumbdrive
- Ran an md5 hash against the file in the iTunes library and the one on the thumbdrive, to ensure they are exactly the same
- Compared playback of the movie via Apple TV gen 3, and the USB thumbdrive plugged directly into the TV
While the movie is still being streamed into the buffer in the Apple TV, there are intermittent video stutters / glitches. The magnitude of the stutters vary, but are still there, ever-so-slightly, and they do continue even after the file is completely in the Apple TV's cache / buffer, although my perception is they are fewer and less severe when the buffereing is completed.
Playback of the same file via the USB thumbdrive is flawless; there is no stutter whatsoever.
No matter how you slice or dice it, the Apple TV has playback glitches; I am convinced of this. It should not matter what the network transport is, or how crappy your wireless signal is, or whether you've secured it with TKIP or AES, or whether its raining outside or not - the Apple TV should not falter on the playback of content that is already present in its buffer, period. Yet it does.
I too hope that this is a software condition, and not something inherent with the Apple TV electronics. Watching the movie via the USB thumbdrive is smooth / pleasant / entertaining, with no anxiety of my mind trying to plow through video glitches. That's the way it should be on the Apple TV too, plain and simple.