So went out and bought an Apple TV, and sure enough, the problem still happens with Apple Lossless and not other content types. More Google searching found the following discussion thread:

http://discussions.apple.com/thread.jspa?messageID=6619589#6619589

If you ask what the dude in this thread and I have in common, it's that we used non-standard tools for encoding our Apple Lossless. Most of mine were ripped by a commercial service (MusicShifter). His were converted from FLAC to Apple Lossless using some third-party tool.

With that as a theory, I found some tunes that I've ripped directly with iTunes versus tunes that were ripped for me by MusicShifter. Sure enough, the ones I ripped myself worked fine.

Okay, easy part done: there's some weird sensitivity to the Apple Lossless file format. Hart part only just beginning: fixing these malformed files!

Thoughts?