I've noticed something similar too but hadn't identified it as being down to the update!
I also notice it on recordings and non HD material.
Should probably do some re-wiring to see if it persists over the SPDIF connection - currently I only use the HDMI.
I've also noticed this crackling sound on HD channels and also on some iplayer programmes. Again only with HD stuff. When I switch to an SD channel the crackling goes but them returns when the original channel is selected.
Because it only happens on the HD channels I doubt it has anything to do with the wiring and is more likely a fault with the HD channels decoding software.
I have found the 10 second skip back button ( |<< ) solves the sound crackle problem, sometimes I need to press it twice but usually once works just fine. Not ideal but better than listening to that awful sound untill they fix the issue :).