I have done this to transcoder all of my BetaSP to Dbeta to embed audio to SDI, but I used my old G4 500MHz laptop to control the io. I do not think that you'd have to remove the io's drivers though. Also you could do this the easy way:
configure the io via the control panel how you would like it, say Svideo and analog 1-2 to SDI embedded. Then disconnect the firewire cable from the io. the io will stay set to the last settings until you power it off and on. Then capture using the io as a non controlled converter box. I have been doing this for about 18 months now, and have had no problems, long before the control panel app. The same works from FCP, just set up the io with the preset you need and then open log and captuer, and unplug the firewire from the io.
Presto, no need to run the control panel at the same time.
The Control Panel is a separate app, so therefore should not conflict with drivers for your PCI card. This configuration works with Kona 2, and theoretically should work with another company's PCI card and drivers as well.
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