Having the latest version of flash always helps as they keep fixing issues with the stage and GPU offloading.
It's definitely not that. I've tried everything from lowering quality to lowest, playing it offline with other decoders, to checking out other recorded sources (including NASA's forwarded webstream) and they all "stutter" at identical timestamps indicating this is really present in the stream going out of Hawthorne (?).
A very recent change was made to get the HD video more fluid and closer to 29.97fps rather than 24/25fps for launch itself.
This, I *think* is the crux of the matter. If you were doing this, decimating 30 fps (OK, 29.97 source video) by a non-integral factor (i.e. everything other than 15 fps, 10 fps) you're bound to run into this kind of skipping. To some people it's not noticeable, but to others the motion discontinuities are among the most annoying video artifacts there are.
Lest I only be criticizing the webcast, I will say that the image sharpness was noticeably better than on the previous launch and pad camera aspect ratios were good.
60fps (59.94) is a bit excessive for web video.
Oh, I definitely agree. While it would make engine plumes dance around more happily, it's definitely overkill for everything else including player performance requirements.
There is DVR now 
Yep, and it's a very cool feature. Something I haven't seen with any other launch webcasts yet so kudos for implementing it.