regarding the MIDI control of FX blocks BYPASS, Eclipse needs to see a transition from at least 0>65 of the MIDI range to change bypass status. Usually when you hit a MIDI switch the transition goes from 0 to 127 (or 1 to 128) and tha's fine… but this transition must immediately fall down to 0 so that the next tie the unit sees the same transition it will change the bypass staus again. In simple words you need a switch that can work in unlatched mode, that is it doesn't stay on 128 after being pressed.
Many MIDI pedalboard allow to configure switches as latch or unlatched.
As for the other problems you are having, please confirm the exact 3.5 version you have installed and provide the unit serial number. We'll look into this.
all the best