Hi joevt. Sorry about not updating this. If you recall my issues are exactly the same down to GPU configuration (except you have a radeon and I have a newer gtx).
I eventually gave up - I called OWC and they could not reproduce the problem. The same issue remains - when the Accelsior is in slot 2, my GPU (other than the 8800gt which works) in slot 1, Windows will NOT boot. Even updated to windows 8 which fixed a whole bunch of other windows issues but not this one. I think it is specific to the 2008 mac pros, which had a unique pci slot configuration I think - the next year added faster slots (pci express 2.0 for all 4 slots I think). The controller is probably having issues with the accelsior in some way.
FWIW, I have noticed that certain other configurations, while they do work, can cause significant delays in booting windows. For example, I have a cheap USB3 card that works in any slot, but when in slot 2 it can take a full minute to initialize (on bios screen a driver message eventually comes up - seems like cards that display such a message can have issues in slot 2, whatever that means if anything).
Eventually I took the accelsior to another computer (a pc) and swapped out the standard 2.5" ssd in that computer to the mac pro. Of course with sata3gb I don't get the same speed as the accelsior in an x16 slot but it's still fast.
Really what I need is a new computer with modern busses, and it looks more and more like that will be a custom built windows box.
Sorry apple, but your direction and my needs don't line up anymore. It's sad but only a little.