[eepunk]

Are you using Ghost or a similar product to backup between re-installs?

I can't say how much time products like these have saved me.

Have you tried shifting the cards around in different PCI slots. It's old voodoo but it still sometimes works.

As regards your other problems, stuttering and so on.

Make sure DMA is enabled for IDE, distance any wireless network broadcast devices, make sure your PC is high-powered enough to handle what you want to do, make sure your graphics drivers/graphics card are DXva compatible.

Does the stuttering problem occur only with playback or does it also affect recorded material?

What CPU usage are you getting with both cards running?

A few more facts and maybe we can narrow this down.