I had a similar sounding problem that I noticed mainly with flash. This may not be your problem, but is an easy thing to check. The problem was the ubuntu ondemand cpu profile is a little, err, too 'lazy'. It doesn't speed up fast enough when you need the cpu power.
The simplest workaround is to try adding the CPU frequency scaling monitor
to your panel. Set the profile to 'Performance' in the applet, and then try running the video etc again.
I'm running 9.04. I thought I had read that this was fixed in 9.10 but could be wrong....