It is normal for the fan(s) to change speeds as the CPU heats up. In fact, you want that to happen or overheating will occur. There are some monitoring programs that may be of interest to you.

PC Alert 4 will show you what the temps are of your PC case and CPU. It also shows other things such as voltage. You can't override anything but you can see what is happening when the noise starts - probably a rise in temp.

Speedfan does the same but lets you tweak the fan speeds. It won't let you damage by undercooling. I don't see the purpose but I'm sure some people love doing this stuff.

Best bet would be to clean out the dust from your fans and heat sinks and see if that helps. If not, fans are cheap to replace.

Rachael