Yea, I realized after I posted that my suggestion was prob not helpful as it seems you already have that figured anyway. Only other two thoughts I have before I am stumped:
My FXII defaulted to CC#34 for scene changes, but can't remember if my FX3 defaulted or if I had to set it - worth a triple check I guess (Setup, MIDI, last page Other). I expect you have already checked this, so -
I send Scene changes as a sep Preset from BandHelper (that way I can send any Preset then any Scene combination); so in my list I send Preset, then Scene. Any chance you are trying to send both in the same Preset, and if so maybe check BandHelper config to see which it is sending first? Might be sending CC, then PC which might look like it wasn't working when it really is?