This strange interaction with the cards, and which PCIe slot they occupy, is baffling ... but I don't know how much time I want to spend figuring it all out.
It is probably a moot point for me, however, unless the hardware RAID proves to be amazing. Other than doing some tests for my own amusement, my true goal was to continue using the Tempo Pro card for my photo library in RAID-0, and use the Tempo DUO card as a Windows boot and OS X boot on a single slot. That is my next test.
The blade PCI SSDs are another option, but I don't think for what I do that I would see any benefit in real use ... just faster benchmark tests. Plus, I see that delivery on the parts from eBay could actually extend out a month or two, which is a lot of waiting. I already have the standard SATA III parts in hand, and I am sure that they are plenty fast for my usage.