This is strange, as I have been running a TimeFactor then an Eclipse and Space in my rig controlled by an MFC-101 and not had a problem like this.

I had it set up like this until recently (just got an H9 and not had time to integrate it yet)

MFC-101 > cat5 > Axe-FX II > MIDI out/thru> Eclipse> MIDI out> Space

Midi channels set on the device AND on the MFC:-

Axe-FX II – 1

Eclipse – 2

Space – 3

Then on the Program change on the MFC-101 I left it as default, so 1 would be preset 1 on the Axe-FX, preset 1 on the Eclipse and preset 1 on the Space.

This worked for me, but in this set up I was not creating any midi merge or signal loops.

What is you midi signal chain?