Hi hangacsimarton, and welcome on this board.
this click noise is related to relay switches. you can hear them, as you mentioned, when activating speaker b from phone 2, reamp, phono...
you can indeed hear it , when it doesn't manage to boot up, like when powering it using usb connection only, on a usb host which is not providing enough power. Was it your case?
hope it helps,
best,