I know this was three months ago, but I thought I would update the thread just for anyone else who may come across it with a similar situation
So in these 3 months I upgraded...
CPU to Core i7 920
RAM to 4GB
Motherboard to ASUS P6T, and now currently using Gigabyte GA-X58A-UD3R
Graphics card to ATI 5770 and now currently using Nvidia GTX260
...and I still had the stuttering black out problem.
Then the other week I set up four WD 7200rpm hard drives RAID 0, and bingo! It works flawlessly now. So it appears just using one drive was too slow for my needs.
I have have since stopped using Fraps as the file sizes were just ridiculous. I now use Windows Media Encoder 64-bit to capture from the AverTV HDMI card. Imo much better in terms of video quality, cpu load and file size. Only nag is that you gotta input audio seperatly as WME doesn't detect it through the capture card.