when you capture HD video with the rtx2 using the matrox codec setting. can you see a difference in quality vs normal captured footage not using the matrox codec settings.

There should be no difference in quality, and if any, using a separate Matrox codec could cause a loss in acquistion quality. Capturing HDV natively over firewire is the highest possible acquisition quality after it is written to tape. It is an unmodified bit for bit copy of the recorded data (in HDV compression).