Hi Lukas, I believe I have somewhat solved the issue, it was possibly related to RFI, so In placed ferrites on the cables to reduce noise. In addition, the microphones I was using were creating input interference, so I tried many different microphones and found one suitable. High gain microphones such as condenser microphones seem to work better than Dynamic, but with the Condenser, I have to reduce the gain almost to zero to eliminate the issues.
I found no issues transmitting with the tune or two tones, it appeared to be a clean signal. I also tried using another computer and it produced the same results.
Thank you for the assistance.