Is the clicking only happening during playback, or is it doing this all the time even when not in use and the avr is off? Turn it to the "on" position and see if it stops, if it does then yes the auto on/off is acting up,,,,, the clicking is the relay.
First thing i'd try is to bump up the AVR sub trim. I dont know how yours is calibrated but if properly,,, you should have room to add 5/6DB's,,,,,, when doing that go to the sub amp and reduce output by the same 5/6DB's.
Another option if your sub has this feature is use the "12 volt trigger" plug and program your avr and when you shut off your avr it will shut off your sub, when your avr is on your sub is on full time bypassing the auto feature.
U can always open up the sub amp if all else fails and see if there is a fuse,,,,, as well as giving your avr a factory reset.
-Funk 21.0LX Master/Slave combo 4800 watts RMS/9600watts (peak)-
-Chane A-2.4 L/C/R
-Chane A-1.4 side/rear surrounds.