If you could please log a bug in the adobe bug base this will give us a way to start the investigation on your specific issue.
If you could please be sure to include a URL which clearly demonstrates your issue. Also, please include OS, OS version, as well as Browser and Browser version. Any info you can provide about your sound card and sound card driver version will also be very useful. The following FAQ page provides instructions on how to gather audio and video display information for you specific OS.
I am sorry for taking so long to reply to your message, but as I suspected I think the problem was unrelated to Flash, and instead caused by other problems with my laptop.
Some days ago I ran a chkdsk on my laptop's hard drive, which immediately seemed to fix the problem, and since then it has not resurfaced. (As well as this I'd noticed the same stuttering when watching DVDs through Windows Media Player, which also makes me think that the problem was not related to Flash.)