Ok, I've struggled with this for a while. I only have the problem when on a high resolution (that's desktop area.) Also I have the problem anytime I have the graphics card is changing what's on my display. Ie. I could be running factorals and maxing my CPU and it'll play no problem, but if I scroll the audio gets choppy. I found the best way to test it is with Windows media player. When I have the visualization showing it's audio and video are choppy. But if I go to another tab or cover up the visualization (or even choose a simple visualization like "bars") the audio is smooth.
I fixed it by doing the following on Windows Vista. I'm not sure if all steps are neccesary but since I can't duplicate the problem anymore I can't narrow down which step fixed it. First I uninstalled and reinstalled my Nvidia graphics drivers. That didn't work. Then I opened the run window and type "msconfig". Disabled all non-microsoft services under the startup tab. Then rebooted. When it came back up I loaded a song in WMP with a crazy visualization running. It got choppy. I opened task manager, displayed processes from all users, then started ending processes. I don't recall which ones I ended first, and you can cause a BSOD so I wouldn't duplicate my steps here. Just go to the SVChost processes. I started ending the SVCHost ones listed as "mine" (my user account was listed under user name) then moved on to the once running under "local" after ending one of them I got an error that the system will have to be shutdown because a process unexpectedly terminated and media player immediatly stopped being choppy. I held down the windows key and tapped "r" to bring up the run box. Then typed "shutdown -a" to cancel the shutdown. (I don't know if the windows-r and shutdown cancel are neccesary.) I closed WMP and after that the system was pretty much locked up. I could open the start menu but no program would run. So I logged off. This locked up completely and I cold booted. When windows came back up the problem was gone.
It was wierd. I have no idea how that fixed it. In fact the computer "expert" in me can think of about a thousand reasons why that shouldn't have fixed it... but it did.
I wouldn't try this unless you have the exact same symptoms. Ie WMP's visualizations cause choppy audio and video not just flash player. One more point. I JUST did this. I yet don't know what other possible effects this had on my PC so this is a definate "do at your own risk."