it works fine here. Eclipse is responding correctly to CCs remoting FX A and B Bypass. If I understand correctly you are sending program changes AND CCs for FX blocks Bypass at the same time. There might be something in that which is causing the problem.
We need an *accurate* description of what exactly is programmed in a switch information you send to Eclipse, including every type of MIDI info (Prog.Ch#/CC#/MIDI channels/etc.).
Also keep in mind that if you have a rig with several MIDI units chained from the MIDI Thru of each one, some information may not get to the target device. In such case a MIDI splitter should be used to manage MIDI info in parallel streams. Try all your tests connecting the MIDI pedalboard directly to the Eclipse, nothing else in between.