The problem is not ATI. It has to be either the card you have (ie something physically wrong with it, damaged etc.) or it's a motherboard problem. I have an X800 XT PE, and when running Doom 3 set at High Quality/1024x768/4x AA and 8x AF, I hit 61 fps(with CAT 5.1, CAT 4.9 - 58 fps).
Now given my card has a mildly higher mem clock and core speed, but there shouldn't be THAT big of a difference. On Doom 3 with the latest drivers, your card should be hitting AT LEAST mid 40's. My "old" 9700 pro hits 21 fps at those settings!
I suggest you throw in an older card and test it to rule anything else out and if it indeed turns out to be your X800 pro, send it back to ATI. It should still be under warranty. Even if it isn't, ATI will repair any of their graphics cards that are less than 5 years old for free, all you pay is shipping. I just hate to see you blow another $300- $400 on a GPU that is essentially equal to the one you have now.
BTW - on Far Cry my X800 XT PE smokes the 6800GT AND the 6800Ultra, Very High Quality/1024x768/ 4x AA/AF - 70 fps! The GT and Ultra hit 53 and 59 fps respectively (according to tomshardware.com).