When I'm on desktop or any where in my PC for that matter I hear what sounds like a helicopter way in the background fading in and out. Does anyone have any idea what is causing this? Thanks for any input! I'm using Bose 2.1 speakers

Not really clear about the problem. Is it the PC (machine) that is making the sound or the audio system? Does the sound persist with the speakers unplugged? Noise from the PC itself is almost always from a mechanical part: bearings in fans or drives stepping motor or head movement in the drive etc. Noise in the audio system is usually from electrical interference of some sort, since digital noise is pretty hard to produce except via software.

First check there are no HF radio transmitters in the near, such as mobile phones. To check that, connect the speaker to some other source (mp3 player for example).
 
It case the noise comes from computer, it is most likely an interference from motors. HDD/CD/cooler. I could never find out either it comes more throw "air" or throw power circuit. On some computers it is too loud, on some acceptable. But the only solution to completely eliminate it is to avoid build in / internal sound card.
 
But what you can in existing setup:

1. Check that inputs are not mixed into output. So, in your software mixer switch off/pull down all volumes from all inputs (line input, mic, CD, etc..) Even when not delivering the signal, they deliver noise.
2. In case you have front panel audio connectors, you can test without the wires connected to the sound card. These wires can work like antenna for interferences.
3. With HDD/CD it is easy to check, just disconnect them (without HDD the system will not boot, but that is not important for the test). I DO NOT recommend disconnecting CPU cooler, even for short time !. But in case you have other (case) coolers, you can try to disconnect them. If you have other power supply, try it.

Its there when I turn on the Line 6 X-3. When the line 6 is off the sound is gone. It didn't do this before. The flutter(helicopter) sound shows up in my tracks after I record also. Very frustrating!

If you listen to the very end of Windy and Warm you will hear the sound I'm talking about. It's a pretty loud flutter sound. If know how to fix this please let me know. It's on everything I record when there is a silent spot in the the song I'm doing
 
P.S. to hear Windy and Warm hit the songs link below

Bill, it looks like the Line6 X-3 is the culprit......are the drivers upto date on the Line 6 X-3? If yes, then possibly try installing the previous version of drivers.
Also, if you had another audio interface to test this out with, you could eliminate if it's the Line6 X-3. 

Is the Line 6 X3 a POD X3 (I have one).  If you turn down either the drive, tone volume or master volume does it go away?  Does it happen with any particular tone or any tone?

Thanks Mesh and fireberd for responding!
 
Mesh - I'll check the drivers
fireberd - I notice that it does it while I'm playing and a few seconds afterward. then It dies down and is silent. It's trails anything I play and is in the recordings

Do you have a reverb or delay setting?  Maybe that is lingering and finally dies down?

Well it's not the Pod X3. It seems to be an effects trail of some kind that is on the soft synths too. The same sound was there after I play something using the keyboard. This is baffling and annoying. The problem is it's on any recordings I do