Is this "fairly new CPU cooler" that you have making contact with the top of the CPU correctly and have you checked the CPU temperature?
Do this with the CPU cooler attached and the fan still plugged in and running.
If you enter the BIOS set-up you should find a system monitoring section. Once you've found it turn the PC off and allow it to cool down for 10 minutes then turn it back on, enter the BIOS set-up and quickly navigate to the above section. Leave it there and watch the CPU temperature to see if it rises drastically.
Don't be alarmed if the CPU temperature rises a little above the norm, this will be because modern BIOSes still don't correctly tell CPUs to idle which causes them to always run at full-whack. What you're looking for is for it to rapidly rise beyond 80 or even 90°C or worse still switch off (or hangs as it may well be). If it does, then there is something wrong with the CPU cooler installation and you'll be wanting to have a look at it.
If the temperature doesn't rise rapidly and sticks around 50~60°C you can safely assume the cooler is doing it's job.
EDITED: 28 Aug 2011 16:39 by MATT