It would be worthwhile to check if the receiver is a high current ie. high signal to noise ratio design . Sometimes high current processor or receivers don't interact well and can cause the problems you have been reporting. It may be affecting the auto circuit on the 350. The EP subs for example also have a high current design and can be more sensitive to calibrate with certain high current receivers/processors. I have not experienced any muting with the EP subs.
I have an old Yamaha sub lying around which had a problem with muting and auto-start. My simple solution was to just leave it on since it consumed little power at idle.
