clicking noise - need help

Hi,
I do have a ht system with pre, sub and amps and a stereo pre integrated by unity gain.
now i wanted to change subwofer-setup from processor-lfe to line in, using either amp-loop by my mc452 or second main out of my arc ls-27.
in both cases there is a loud clicking noise when switch mute on/off or channel of ls-27 pre.
anybody s got an idea?
is the unity-gain loop the problem?
using lfe of processor works perfectly without noise. but i would like to support deep bass by sub with my stereo
subwoofer is velodyne 12+
Thanks
oliver