I found when I starting using my Axe3 live, I had to be very careful when setting up my scenes so that I was using the correct channel in each scene. An example is, I would add a wah block to my patch, set it up as auto engage on Scene 1 with Channel B, but forget to check which channel the wah block was set to on Scenes 2 - 8. Then it would work fine on Scene 1, but as soon as I switch to Scene 2 then the wah would come on.
So now my process is, every single time I play live, I first go through all my scenes to make sure they are set to the correct channels. An easy way to do this is to use Block Info on Axe Edit.