You would need to set the type to None (as opposed to Drive1, Scene 1, ...). You can the program two different midi messages to send when the button is engaged/disengaged.
what have you setup to make it change to Scene 2 on that IA?
Which MIDI channel is the Axe-FX set to? You need to use separate channels for this to work correctly, or else the PC for your amp would be changing Axe-FX presets too. It sounds like the Axe-FX is probably on a channel other than 1.
I guess that should work. Did you verify that scene select is set to CC#34 at the Axe-FX I/O: CTRL page?
CCs still work with Prog Change = off. Axe-FX mode and total sync shouldn't cause this either. If separate channels doesn't solve it I'd try disabling the PC to see if the scene CC alone will change scenes.