Hi Scott
I assume you have tried effects units plugged into a Bose PAS using both methods(1 click and 2).

I don't profess to know the phase cancellation problem. Just a thought.

Bernie
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pa4X 76 ,SX900, Audya 76,Yamaha S970 , vArranger, Hammond SK1, Ketron SD40, Centerpoint Space Station, Bose compact