Are you saying the sub does not come on when you turn the amp on or that it does not come on at all when you watch a film.
It could be that the volume level is set too high on the sub and the amp has set the LFE so low that it will not trigger the auto power on for the sub.
My sub volume is set at the 10 o'clock position and the amp has set the LFE to -3.5 but it does kick in when needed not when I switch the amp on.
The other thing to check would be the frequency selector position, check the manual for the sub that this is set correctly.
Re run the auto setup once you have made the changes.
Edit: just had a look at the manual page 9.
Standby:
In this position, the amplifier is in permanent
standby, and the light glows red.
If, when set to Auto, the subwoofer should
repeatedly go into standby mode when
playing programme via the LINE IN socket,
try reducing the volume setting on the
subwoofer and restoring the balance by
increasing the subwoofer output of the
processor.
So if you re run auto setup it should pick up the reduction in volume from the sub. If this does not work go into the amps setup menu and increase the LFE output i.e. if LFE on amp is - 3.5 try setting it at 0 and try watching a film again.
Please make sure you have a film that you know has a good bass to it.
I would also try setting the frequency control all the way over to 140 Hz and let the amp take care of this as well.