In stock form, the two are very similar. Don't know what your flash may have done. I was looking at these two cards, and actually bought a 5900XT but couldn't get it to install. I tried a 9700pro and couldn't get that to work either. I finally got the 9700pro to work after formatting and doing a clean install of windows, and I sold the 5900XT to a friend. When I bought the cards, they were all around $190-$200, with the 9700pro at the higher end of the scale. I think the 9700pro is a bit faster, especially when you anable AA and AF, but I don't know how significant the difference is.
I like the 9700pro, but I prefer the Nvidia driver interface and the ease with which you can overclock the 5900XT. When we intalled the card in my friends computer we got a nice little overclock right out of the box (after enabling something in the registry, I forget exactly what, but it exposed an overclocking utility build in to the Nvidia driver). I would have been happy with either card, but then I was coming from a GF3 Ti200, so either card was a huge improvement.
-D'oh!