[From what I've seen, there are a few good ways to get your temp. By far the best way is through your BIOS - this should be the most accurate reading. Of course you won't get to play around with it too much. I personally use SpeedFan to check on my temps while I casually run through my programs - its got a great feature that lets you keep an eye on your CPU (or whatever temp you want to watch) by setting it in the sys task bar (bottom right corner windows).
Also, I use
SiSoft Sandra especially to test my CPU, etc on temps (burn-ins). If you are currently at 41C CPU and you are not overclocking, I wouldn't worry about it too much.
That being said, if your system temp is also at 41C either you have a really kick $@# cooling system that isn't working just right (e.g. your cpu is staying at system temp) or your sensors are goofy. You may want to check that you are getting enough output from the back of your box (i.e. getting the heated air out). Or maybe you are just in a really really hot room that won't let you system get any cooler anyway????
Just some thoughts