I think as others suggested you need to narrow down the source of this. This isn't the typical intermod that I hear, and, suspect this could be leased line related - but there is not enough information in your post about how the system is constructed. Instead - i'll give you how I'd troubleshoot the issue.
With the issue happening:
What happens when you disconnect your console and listen with a buttset? Do you hear the noise?
What happens when you disconnect the tone remote adapter and listen on the end of the copper going to the console? Do you hear the noise?
What happens when you listen from the pins on the back of your repeater / voter? Do you hear the noise?
Does the voter indicate what site the audio comes in on?
Can you isolate this to a site by turning them off/on via the boter while the noise is happening? With bringing the sites up/down can you make it go away?
Can you listen to the audio from each site while it is happening using a buttset?
Does it happen on every site?
What happens if you bypass the voter and run in-cabinet repeat? Does the sound continue to happen?
Have you been up to each site with a spectrum analyzer to look for on-channel nose?
Have you looked at your MUX's (if you are running Fiber, T1, etc,. to see if you can isolate it to a port? Try listening to the DS0's using a T1 tester and see if you hear the noise on the DS0's if it's a T1.
Can you change out the ITA and the power supply?
Reseat cards in the Voter (kind of spectratac thing to do - but almost like every now and again you have to turn the pots to keep them happy, this might be similar in a GE voter?
Have you done an intermod study at all your sites?
Do you have any BDA's or Emergency Responder Radio Coverage systems in place? (oh you'll see these on a spec an at your master transmit site pretty clearly - and if you find noise external to your system there is a REALLY high chance these are to blame...)
Have you gone through your duplexers with a service monitor lately?
Check any RX Filters or Multicouplers? If you are using those scanner multicouplers that one of our local vendors LOVES to sell w/out filtering........ blame that.
How about checking antennas? VSWR, Return Loss, and DTF? Compare it to last PM.
Do you have Triple Circulators on everything?
Alex