I know that it's not the fan or the vents as I have cleaned them out multiple times already. After doing some reading and google searching, I found out that this is probably a Linux specific problem.

I have an HP probook 4540s and when running in Linux, the laptop gets very hot, even when performing simple and less demanding tasks like word processing. It even gets hot when hooked up to a charger. I think it's a Linux specific problem because Linux tends to over drive the processors and make them get very hot, while in Windows where the correct drivers for the processors are installed instead tend to keep the processor under control and free from throttling itself. What are the drivers needed for this laptop in order to keep the processor from over heating. I have an Intel Core i3.

For Debian, check if cpufrequtils is installed.
https://wiki.debian.org/HowTo/CpuFrequencyScaling

Is this going to slow down my processor so it doesn't create heat, There should be a program on there that would control how much processing power it uses instead of making it use everything all at once.

Among the laptops I have is a Core I-3 and I've run many distros with no runaway cpu or heat issues. What DE are you using? Many programs will show you what the cpu cores are doing and whether they are running wild. Does this laptop have nvidia graphics?

All of mine run in "on demand" mode where the cpu only runs full speed when necessary...

I have backbox running, It's an HP Probook 4540s with intel graphics, I just noticed that the fan isn't spinning (I can't hear it. I am wondering if this is a hardware issue or a linux thing. I used to hear the fan go crazy in this thing but I don't hear it anymore). I just recently bought a new charger and up until now it stopped working. I checked the power specs on the charger brick and they are the same as they were on the older charger that I lost. Can leaving it out of use all this time make it stop working. When I left it off for that long period of time it was on suspend. I think I might have screwed something up here). I'm going to check to see if a dirty fan is my problem but for the time being, what else do you think it could be?

I just opened the laptop and powered it on to look at the fan, the fan nudges a little bit and then refuses to spin. I think something might have burned out or something. I am wondering how I should fix this. A new thread (or moving this thread) to hardware might be helpful.

I guess I might have run the fan out as it was running while in suspend. I should've known better

Most times the fan access involves removing the heatsync from the cpu. It may be bound up with dust / hair / cat fur. A can of compressed air can help give it new life. Although a fanned platform could take it's place without a need for software support. Most times the cost of replacement is more than a new laptop. And the replacement parts is likely to be "used". A fanned platform was like $10 at radioshack last time I got one.

Sounds like the bearing froze up. Replace the fan.

Sowing Machine oil or lightweight thin oil drop on bearing then try turning it on. If it spins. The fix won't last. Replace the fan.

I sprayed some compressed air into the fan and no dice.

I re-installed windows in it and the fan just started working (after several reboots that is) so I am guessing that it might either be a bios problem or a hardware problem. The computer is still under warranty and I called HP technical support last night and they are sending me a new fan in a couple days. The fan is spinning now but not as fast as it used to so a new fan might be good but in the meantime I'm just going to assume that it's a hardware issue and might need a bios update.

If having the fan work in windows and not Linux is the case here, How do I get it to work in Linux again? Is there a kernel patch or a driver that I need to install in order to get it working. I am thinking that the bios must be pulsing the fan upon startup (It just twitches for a partial second, I think the bio is checking if it's there, then the fan starts up when windows starts up. How Do I get this done in Linux).

This is starting to look more like a problem with Linux and not a problem with the laptop hardware. I am now wondering why Linux isn't letting the fan spin after bootup. The fan doesn't spin apparently after the splash screen shows like I expected to. Nevertheless I'm going to install a new fan but I am still wondering why Linux isn't letting the fan spin.

All of my computers are laptops, 4 of them, and the fans work as they're supposed to in Windows & Linux. In general, a temperature sensor controls the fans unless overridden by a BIOS entry. I've used a variety of modern Linux distros and have never had fan issues. One of mine is an HP EliteBook 8440P and it works as it should.

I had huge issues with a hp fan. Mine was roaring, and the cpu was crawling. I was about to start hacking the dsdt, but it turned out to be the kernel and boy was I glad I left the dsdt alone.

I have 3.11.0-24-generic kernel. What do you suggest I do? It's the latest kernel update for the distro I am using. I am willing to change my distro but I think that all of the recent ones use the same kernel.

I installed the fancontrol package and there doesn't seem to be any fan control since it continues to get hot and the fan isn't running when it gets hot. What do I need to do from then on after I had installed all of the fancontrol packages?

Well, I just tried to install and configure the fancontrol program, but by the time I ran the pwmconfig command, it said that I didn't have pwm-capable sensor modules installed. even though the sensor command detected some pwm devices.
It doesn't seem to have anything there to help control the fan and make it work whenever the computer gets hot. I was wondering if it was in the bios but there doesn't seem to be a setting in there for that. I am getting the new fan installed to see if that may be the case as to why it keeps stopping and making my laptop get hot. The fan works it just keeps shutting off randomly when booted in Linux and when it gets hot it doesn't turn on. I also want to know that even if the fan control hasn't been set, what is my computer set to as far as temperature to control the fan whenever the circuity reaches a certain temperature and decides it needs to turn the fan on.