i have had this issue before .
once it was something was touching the chassis
once it was the circuit board "flexed" a bit when it was screwed down becaus ethe holes for the standoffs were not lined up perfect , so i expanded the pcb holes with a drill .
the other was that 2 jacks on the circuit were never intended to be grounded , so when i modded it with metal jacks , it worked till it was in the chassis , at that point it all grounded .
i would suggest removing it to see if it fixes , to make sure , then take it slow from there . start reinstalling it but checking it as you go , one step at a time , if possible .
good luck .