Hey I have a similar issue. I think it's something to do with the lagarith lossless codec but any clarification would be great.
I use VLC to play back 60 fps recordings, however if I play them fullscreen I'll get stuttering. I know it's not corruption on the video file, as I can make the screen to a smaller window size and it'll play back the same part of the video nice'n smooth. (Strange technology)
You may say just play them all in the windowed size and problem solved right? Yes, but it's highly annoying.. and I like to watch full screen. Sometimes I can play the video fullscreen choppy for about a minute, then it'll (settle in?) like it's gotten used to it and start playing the video back properly at 60 fps.
When importing the file into premiere pro or any other video software the video will play back fine, and render perfectly once edited.
I doubt my hardware is causing any of this and think it may well be a glitch of somekind that has been overlooked.
Oh and when I play back in Windows Media Player, I don't even get video just sound. But I guess that's down to not having the right codecs in WMP?
i7 3770k
R9 280X
Z77 GA-13 Mobo
250 HyperX Kingston SSD
3TB WD Caviar Green HD (Drive where I record and playback video)
Windows 7 Ultimate