I think you should put an dummy plug on the second card which would activate the card for windhoos
Or, " but this is a easy fix which can fail if the system gets rebooted " go into your desktop settings and extend your desktop, which would turn again the card active for windows and poof it should mine away
Windhoos sets a card inactive if no video plug is attached to it hence the dummy plugs, i never want to run without them anymore. Even when a screen is attached i put a dummy plug on it since the wife went with a vacuum cleaner behind it and the cable fell off xD
No plug to a screen or dummy means its not being used to windhoos, so it turns the card off to save power and such.
Where do you get your misinformation? You only required dummy plugs pre 11.6 and thats on ANY os including linux. Any driver version above this does not require dummy plugs.
Also, "Windhoos" does not set anything, the ATI drive does and only that.