I have a similar setup with a SYN-1 into a head's loop (4CM)- bypass on the SYN-1 it still runs the effects from my pedal board, no issues, with our without the footswitch. I actually run "double 4CM" with both a SYN-1 and a Line 6 HX Effects, and it allows my pedalboard to route signal chain to the input or loop of either the SYN-1 or the head, very flexible.
I'd unplug all your patch cables, and reconnect as per the SYN-2 manual, and maybe test all your cables individually. Can't tell you how many times I've been punchy tired & had a patch cable connected wrong, convinced something was broken, only to start over & find a wrong connection.