I have an extremely similar problem on my JTV-69S Variax guitar. When it is "on" and in modelling mode, the pickup selector locations for mid-neck and mid-bridge (so 2 and 4) do not change the modelled guitar. It just stays at whatever guitar model it was last on. This is easily confirmed by connecting the guitar to my HELIX, and then connecting my HELIX to my computer running Workbench HD (the model doesn't change). If I press the pickup selector "into" the guitar body for a moment, the model changes until I remove the pressure. The pickup selector works as expected when the guitar is not in modelling mode.
I'm a little odd, so I own basically two of the same guitar. My older, JTV-69 (note: no "S" in the model name) still works great, as of now.
