[WisdomWolf]

daily show and colbert report are encoded at 60 fps which the apple tv can have trouble playing back. the xvid version is 30 fps and should play fine.

http://forum.xbmc.org/showthread.php?tid=103957

The problem that he is having appears to be with the SD versions of the show based on his log. I have the same issue with the Daily Show, but the hiccup errors only seem to appear on SD at 30fps, all the 24fps stuff plays fine. I'm still on 5.0, but have the same problem. After perusing the log a bit for differences between The Daily Show/Colbert Report vs Glee (which I assume is the SD show that worked) the only difference I noticed was this:

23:02:20 T:133009408 DEBUG: CDVDPlayer::HandleMessages - player started 2
23:02:20 T:133009408 DEBUG: CDVDPlayer::SetCaching - caching state 3

The first two both started with caching state 0. I have no idea if this is relevant, but that's the only immediate difference I noticed.

EDIT: I went ahead and enable debug logging on my install and tested some videos. I don't see anything in the logs, but I did notice that the onscreen debug text indicated that the fps never went over 28fps, even though cpu was never maxed. Not quite sure what's limiting it, but a display rate that's less than the video frame rate seems like the most obvious cause of the stutter.

UPDATE: After playing around with the settings it appears that the combination between 30fps material and upscaling is the issue. When I changed the view mode to original size (which is a tiny box in the middle of the screen) the video plays without stutter.