Guessing will help nobody. Put some heavy load on the CPU (yes, that means when the CPU is under stress) for several minutes and have a look at the temperature while it is under heavy load. For example compile a large software with many threads, render a 3D image or encode a movie/some MP3s.

Under kind of a heavy load, I mean when I am loading a game it goes up to 54 degrees.

54° Celsius is totally normal, nothing to worry about, so I don't think that it is CPU related.

I ran a .mkv to .avi encode and it beeped once but the temperature was still 54-57 degrees.

What could it be then ?

At the encoding task the CPU monitor shows 50-60 percent use.

---------- Post added 07-16-11 at 01:04 PM ----------

Maybe I should run a program with an infinite loop?

It beeped while at 0 percent in use, temperature 49 degrees. I was typing in terminal. I have no idea what it is ...

I ran a program with an infinite loop and while going up to 50 percent in use it beeped.

Isn't there some kind of test for the whole computer that I could use ?

I have a suspicion that it is the operating system's fault. I might have done something to upset it. I ran an Ubuntu live CD and ran cpuburn. It only stressed it till 50 something percent, not 90 something. But it didn't beep while I was using that. It didn't start beeping until recently anyway so it must be something I've done. I'll try to reinstall the system and see if it still beeps. But I can't do that until Monday.

Yes you can try reinstalling the OS as well as you can give a try installing Windows 7 (which is supported by most of the vendors and does come pre-installed with most of the laptops today).

As you said that it is a brand new laptop I would suggest you should better contact the vendor and tell them the symptoms (I expect their first question to be which OS you are using). After testing with different OS on Monday a you said and if your system still have the beep issue you can let them know that you have tried this with couple of OS with same result.

Yeah, I have a recovery CD with windows 7. First I'll reinstall fedora and if it persists I will install windows. Hope for the best.