One thing you want to do while you are booting Windows from a drive bay, be sure the DUO card is installed in a slot so that Windows can detect it and load any required drivers for the card. Then, it should be a simple move of the SSD from the drive tray to the DUO card and boot it up (at least it was for mine).
Hey mate. Yes, I've already done that with no success. I have been in dialogue with Eric from Apricorn who do his own system tests for days with Mac Pro 3,1 and Duo with Win 7 and Win 10 and could not get a consistent successful result. However he had no issues with the Mac Pro 5,1 booting correctly. He also said that other are still having issues booting from this card on 3,1's.
I don't know what you guys are doing on your Mac Pro 3,1's to get it to boot. I'd love to know.
My intention is to have 2 x SSD's on the DUO. One with OSX Mavericks or Sierra, and the other with Windows 10 or 7...whatever will boot and work reliably every time. On a 3,1 system. Any takers who have done this successfully on this exact system model ??