My computer is whining

Are you hearing it from your speakers or the computer case?
 
If it sounds like the computer case (hardware like you mentioned)...
If you have AI Suite II loaded on your machine, pop it open, hold the "Monitor" button, and "Sensor." High pitch whining can come from a hot CPU or GPU (graphics card). If you are running anything "intense" CPU or graphics related, that could be the source. If you are not running anything intensive, check the temperature on the CPU... the thermal paste between the CPU and the cooler can degrade over time. (this issue is generally VERY high pitch, like a squeal)
 
Other hardware issues (less critical) can be things like dirty/imbalanced fans, but the frequency is often not extremely high.
 

If from speakers is less concern than the box itself. I was worried you may be having a heating issues, so glad you confirmed the source. Something from the speaker could very well be cross-talk, or degradation in a piece of gear. The next part would be trying to isolate it.
 
Some hardware knobs(pots) and faders will oxidize and can cause this. I quick check on the hardware would be to cycle knobs and faders several times to wear off some of this oxidation.
 
Cross-talk can be another alternative, or potential damage to cabling (something like a cable you may have rolled over with an office chair wheel). Events like that can potentially split insulation on the wires internal to the outer covering. Also, something that transmits RF or even an ionizing air filter too close to equipment can cause cross-talk.
 
Is this something that shows up in an Audio track in X3 if armed (i.e. could you record it)? How frequently does this occur?
 
FWIW, my 15 yo interface (which I still use as a MIDI input), has internal degradation that actually shows up as intermittent flashing on the "Signal clipping" LED (with nothing connected to it), so try to isolate pieces of hardware from the loop (or check the environment for changes which may be inserting the noise).
 
 
 
 

mettelus
If from speakers is less concern than the box itself. I was worried you may be having a heating issues, so glad you confirmed the source. Something from the speaker could very well be cross-talk, or degradation in a piece of gear. The next part would be trying to isolate it.
 
Some hardware knobs(pots) and faders will oxidize and can cause this. I quick check on the hardware would be to cycle knobs and faders several times to wear off some of this oxidation.
 
Cross-talk can be another alternative, or potential damage to cabling (something like a cable you may have rolled over with an office chair wheel). Events like that can potentially split insulation on the wires internal to the outer covering. Also, something that transmits RF or even an ionizing air filter too close to equipment can cause cross-talk.
 
Is this something that shows up in an Audio track in X3 if armed (i.e. could you record it)? How frequently does this occur?
 
FWIW, my 15 yo interface (which I still use as a MIDI input), has internal degradation that actually shows up as intermittent flashing on the "Signal clipping" LED (with nothing connected to it), so try to isolate pieces of hardware from the loop (or check the environment for changes which may be inserting the noise).
 
 
 
 

When X3 or S1.2 is not loaded, and my signal chain is my Zoom R24 usb to my PC in and my Zoom line out into my Nano Patch and the Nano Patch out to the Equator D5 powered monitors, I get the high pitch that seems to directly correlate to my harddrive.  When I just down the Zoom, I don't hear it.  So some signal is bleeding into the USB cable from my computer I think!

Have you been able to try another USB port or even another USB cable?
 
Isolating something like this can be tedious and the best way to do so is isolate things one at a time (unfortunately) which is not often feasible.

Have you worked your way backwards, 
Disconnect everything
speakers on -listen
connect speakers to Zoom- volume down --listen --volume up ---listen
Connect Zoom to PC - listen and on and on... 
 
 
Weird sounds can come from unexpected places so the only way to trouble shoot is slowly adding or subtracting until it goes away. 
I had a crackle in my left monitor when playing bass heavy music, I thought the worst, turned out was the AC cord to my sub woofer was loose and somehow sending the crackle to the monitors. Why only the left was the mystery.   

gustabo

Rimshot

gustabo
Are you using balanced or unbalanced cables to connect your speakers to your audio interface?
 

Unbalanced.

Is it possible to try balanced and see if that gets rid of it?
 

My Nano Patch does not have balanced out to the speakers only balanced in.

Do the powered speakers (what brand and model are they) have balanced inputs. There is a way of wiring from unbalanced out (nano Patch) to balanced in that sometimes eliminates noise. It requires you to make a special lead. It might work in your case but you need a proper balanced input for this to work.
 
For example when I connect a stereo mini jack out (IMac) or most computers to two line inputs on my digital mixer (even though my line inputs are balanced) using the normal approach of unbalancing one side of the balanced input, I sometimes get high freq noise like you are describing.
 
I have made a special lead now that connects to the balanced line inputs (not using the normal sleeve earth that is) and this noise is not present when I do it this way. It may work in your case too.