About a month or two ago I noticed that video playback on iTunes (on Windows 7) was stuttering - the audio would remain in sync, but every few seconds the video would stutter or freeze for a moment. Audio files play fine. Tonight I updated to iTunes 10.6.3.25 and the problem is still occurring. I experience this issue even when iTunes is not otherwise busy doing something else, like updating an iOS device etc. I checked the drive and it has heaps of space available.
I was going to check if I needed to defrag my drive when I decided to play the very same m4v file in VLC (2.0.1) - and it plays fine! So how's that for a work-around: I won't watch Apple media files on Apple's player anymore. (Playback on my Apple TV unit also seems fine, so I have that too.)