When I attempt to enable Input #2 in any case, especially when trying to use SCA #1 Output at the same time, StereoTool will go silent, and quickly crash a few seconds later. I'm running the latest JACK StereoTool (9.34) under Ubuntu 18.04.2 LTS.
I attached a screenshot, probably of no help. Of course, the settings are disabled in that screenshot because if I do enable them, it'll crash. I've been attempting to use this feature since the 8.x days to no avail, and finally figured it wasn't on my end and I'd make a bug report. Not sure what other means of information I should provide, so here's some random stuff that may or may nor be helpful:
'jackdmp version 1.9.12 tmpdir /dev/shm protocol 8
Linux version 4.15.0-50-generic (buildd@lcy01-amd64-013) (gcc version 7.3.0 (Ubuntu 7.3.0-16ubuntu3)) #54-Ubuntu SMP Mon May 6 18:46:08 UTC 2019