ST, thanks for the advice. I checked all the slots and they all have the Volume set to "location - output" and range "-5".
I tried it with the volume lock both on and off, nothing changed unfortunately. 
I use it as a final output level and tend to turn the volume down to "off" between songs.
Burkhard, it's a Dunlop volume X expression pedal set Wah>Volume but I also tried it as a dedicated Volume pedal in socket 1 but it's the same result. This not really a performance issue as the volume pedal is always ON somewhere when playing.
I discovered this by accident in rehearsal. I had the volume turned off (at heel) and I was reviewing the stomp switch assignments, so I was selecting each performance slot 1-5 in turn and looking at the screen info. When I selected slot 2, I heard some string noise from the guitar I was holding and realised that that slot was still passing some signal .
Further investigation showed I had a few slots in different performances, that did the same thing.
What I also found is that once a slot triggers the issue, all the other slots in that performance then pass low signal as well. It's as if slot 2 is tweaking the general level up a few dB even though the pedal is physically at heel.
I'll look into doing a backup as you suggest and raise a ticket.