Well I have the most recent bios and my case is not hot as my graphic card idles fairly low. I think it could be a reporting issue when idle because even under a full load the temps barely move. They do move a little but not very much. I can also feel the air from the exhaust is not warm at all. In fact it's fairly cool. So I'm thinking it is a reporting issue. I am using RealTemp and all the temps seem in line with each other with cores 0 and 1 just slightly higher by a degree or so.
Also I saw this picture on the net when searching though not sure what kind of cooling the person had.
His Q9450 C1 stepping is overclocked to 3.6 ghz at a vcore that is lower than mine by default (when set to auto)! His was 1.224 mine 1.265. And his also idles in the 40s. So maybe it's not out of line. It seems like this motherboard by default sets the vcore way too high which obviously results in higher temps.