I don't know for sure because you didn't provide an audio sample, but a possibility could be noise build up from the recording process.
For example:
You record your guitar amp... so of course you have it loud as phugg, distortion on "11" and so on. The amp is buzzing like a mofo because of all the gain. God help you if you have single coil pickups, a semi-hollow body guitar, or microphonic pickups.
Anyways, the amount of noise will be recorded. Let's say the noise floor is somewhere around -32db and your main signal is topping out around -12db. Only 20db of headroom over your noise floor. Not good. (Consequently, also one of the major arguments against recording guitars with a ton of distortion on them regardless of style.)
So, you record another track... and the amount of noise will raise and raise with each consecutive track. So what was just bad before becomes unbearable. If you are recording 4 or 8 tracks of guitars... you have not only overdubbed your guitar parts, but the noise as well!
Once again--god help you if you further compress the guitars as this will reduce your SNR (signal to noise ratio).
Remember that microphones add noise (self noise), as do many preamps. Cheap recording gear will add noise to that as well. Having a monitor or computer near your inputs will add some noise as well... and many types of lamps as well.
Before you know it, you have a noisefest on your hands!
My advice is root out the noise in your electronics, learn to set the amp for your tone in a non-buzzy fashion (reduce the gain), get some power conditioners, get a breakout box for your inputs/outputs to your cpu, make sure to use low self-noise mics, put a noise gate in your guitar setup and so forth.
That's just my guess. I've seen this happen before. The number one enemy to recording good clean guitars is lowering the amount of amp noise as far down as you can get it.
Another tip: when I record guitars I silence between all the gaps using a wave editor such as Sound Forge or WaveLab. This can become annoying if the band plays Pantera ass riffs. I generally do this with all instruments, especially vocals, to eliminate any headphone bleed, noise, boops, bleeps, jet fighters passing overhead, etc.....