So I think I've tracked it down to a power issue. If I take the same card out of the pro and connect it up in a PC with only 6 of the 8 connectors connected (based on the normal 6 pin plug in the mac pro) the PC boots successfully to a black screen.
Doing the same with all 8 connected, card behaves normally. I verified the bios and it is correctly stating the flashed details. So, thinking that for this particular card, I need ALL 8 pins on each connector to be connected, I've ordered 2 6->8 pin cables for a mac pro. I'll get them tomorrow and should be able to retest then.
Well that worked! Once I got the 6->8 pin adapters I can now boot in to OS X able to see both the white boot screens and the OS just fine over HDMI, will be switching to mini display port as soon as my adapter arrives to run an older Apple Cinema display. Note that the output from the DVI port is garbled for some reason as soon as it hits the OS.