4CM noise, any other setup has no noise

Are the pedals using an isolated power source? This is obviously a ground loop issue. I am not surprised that you have a squeal.
yes, they are plugged into the Furman P-1800AR. But again, how come my pedals are the problem when in any other setup they are ok?

I truly think the issue is the axe fx hitting the pre of the amp, possibly amplifying any noise the axe fx makes.
 
yes, they are plugged into the Furman P-1800AR. But again, how come my pedals are the problem when in any other setup they are ok?

I truly think the issue is the axe fx hitting the pre of the amp, possibly amplifying any noise the axe fx makes.

Please post some clips of each combination of gear for proper troubleshooting.

So to confirm, you're not getting any ground loop low frequency hum. Are you just getting the high pitched sustained noise or also a lot of hiss?

I'm guessing you've tested this with the Marshall going into a real cab with just guitar into amp into cab, and then guitar into Axe (with zero effects active) into front of amp only into cab? Does the Axe add hiss to the front end of the amp? If so, double check your digital input gain in the Axe is set correctly, and that the Axe's output is set correctly. There will be a small amount of hiss from the Axe but it shouldn't be a problem. I'm also guessing you're testing this with the Marshall's gain high to be able to hear the hiss more.

I'm pretty sure humbuster cables will only get rid of low frequency ground loop hum but maybe the high pitch sustained thing is a part of a ground loop too.

I used to get a lot of hiss with the Axe II MK I into the front of a Marshall JVM but then had it modded by G66 to the MK II spec to get rid of the hiss (the hiss was caused by Output 2 in the Axe II being wideband). I don't think the Axe III has that issue.

I've also experienced a high pitch sustained noise with the Two Notes Reload and the JVM if i run the JVM's Master and Channel volumes on max.
 
I have experienced something similar (the noise/squealing)... funny enough with a very similar setup. I don't have all the answers as it happened a while back and i haven't played that setup since.

Similar to you, I was using my AFx3 with my JCM800 in ...lets call it pseudo-4CM. the 800 is very old and does not have an effects loop, so i take the speaker out into an X-Load back into the AFx3 and then out to a separate power amp. The power amps weren't the problem; i tried both my Mesa 2:90 and Matrix amps (tube and solid state)... no difference.

Like you i also had a Furman power conditioner involved (not the same one though...). Everything was plugged into it

I was also trying some pedals in-front of the 800. (AFx3->pedals->JCM800) Pedals were powered from a voodoo-lab isolated power supply (plugged into the Furman).

In the end, I got things quite by removing the pedals. I tried all the various combinations of outputs/level settings on the AFx3. I tried different ground lifts.. nothing changed. If i went guitar->pedals->800->-Xload->AFx3... all was good. But i like the hum-reduction/gate on the AFx3 so i took out the pedals. The noise stopped... i didn't follow through to see what was the issue with the pedals...

Funny though this issue your having sounds a lot like my issue. I don't suspect the AFx3 at all; it has never given me any issues on any similar setups... just this one!

Hope this helps!
 
Ground loop. The current choose the path with least resistance to ground. 4CM introduce a net of path. Each cable with flowing current act as an antenna and signal generator. In my experience, an isolation transformer on the culprit cable solve the problem. It happened to me once there was multiple ground loop cable problem in 4CM with a Mesa (solved with dual isolation).
 
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