If you're using IDE hard drives, ensure DMA is enabled for your hard drives. 7200 RPM drives are preferred, but 5400 RPM should work with DMA enabled. DMA is enabled by going to Start -> Settings -> Control Panel -> System -> Device Manager and clicking the plus sign next to "Disk Drives." You should see your hard disk under Disk Drives. Double-click it and click on the Settings tab for the window that's appeared. Make sure that DMA (in the lower righthand corner) is enabled.
Also: check out this link for a ton of helpful info on print-to-tape (some of which also applies to capture).
I was having a related problem with the new capture program. I uninstalled the newer version of Vid. Capture and loaded the older version but that did not improve it until I ran REGCLEAN. That magically resolved my avi playback breakups.