Unless a magical update happens, aka OSX gets fixed... WAKEUP APPLE!!! , The 2009 MP is turning out as the LEMON step child of the product line.
I know you were probably being dramatic, but you can't honestly believe that the current generation Mac Pro is a lemon by any means. While it seems mysterious as to why the temperature is rising more than expected, it doesn't affect the Mac Pro in any discernible way nor does it impact the computer's speed, your workflow, or what you can get out of the machine.
I certainly didn't buy the Mac Pro for it's "green" features, I bought it because it's a powerhouse and I expect it to throw out more hot air than your typical iMac or Mac Mini. There's something in OSX causing the temperature rise, but it will eventually be fixed. I haven't been back to this thread in a while, I'm curious about something... do we know that all of these programs, i.e. iStat Menus, etc., are reading the temperatures properly? I've heard discussions elsewhere that utilities are not properly reading the temperature sensors in the new 2009 Pros. Could that be a possibility?