hey guys… sorry to bump an old topic, but seemed to make more sense than starting again! 
note that i am not referring to ground loop issues here, but rather specifically the periodic low thumping noise that a few folks have written about. with ground loop issues resolved and with good gain-staging, such that both my input and my output signals are close to 0, these noises are at most around -50dB. as such, many folks will have not noticed them and they might be, arguably, within an acceptable range for a lot of use cases – i suspect that’s why this specific issue hasn’t been reported widely.
however, i do a number of things in which silence and low level signals are important, so it has been an issue for me from time to time.
i recently made an important discovery:
if i have a flashing button (i.e. a button assigned to tap tempo), the thumping coincides with the flashes of the button LED. if i change the LED Brightness setting to LOW, the thumping drops about 20dB – that makes a huge difference, and is acceptable for most of my scenarios.
note that there is also a low-frequency “rumbling” associated with rotating any of the encoder knobs; unfortunately no adjustments to the display settings seems to affect that noise. however, it is a lower level and only happens when knobs are moved.
my unit is a Duo X LE. i can’t say whether things are similar on a full production run Duo X.
hope it helps somebody out there!!