I've experimented some curious behavior in Rakarrack (RK). It behaves different when I call it the same way (command line parameters and configuration) but adding parameter "--no-gui".
When I start RK with GUI it reacts (I can see lights in buttons and hear the incoming signal with effects applied) when I switch on/off effects with my pedalboard via MIDI, but If I use it without gui it doesn't respond to any switching (you can here the incoming untouched).
This didn't happen before, I think. So maybe it has to do with the fact that I changed recently RK's MIDI listening channel to 16, instead of channel 1 by default. So maybe this issue has to do with Rakarrack not taking the configuration. I've checked configuration file when running without gui and it is what I configured, just reading it in a text editor, it's the same as with gui.