I too noticed this bug after the latest update (Maybe I didnt notice it before).  Not only does the volume drop when switching between some of the presets with the toggle switch, but I also noticed the volume drop with the acoustic models. 

For example: If I am playing with mags and press my model knob (already on the Acoustic Bank), my acoustic has very little volume, but if I change the model knob or toggle, and then switch back to the original setting, then the volume is normal. 

I was playing a gig last night and had to switch from mags to my acoustic model and the volume was not there.  I was starting off the song, and it was ruined bacuse you couldnt hear me.  Then I had to stop what I was playing and "Fix" my acoustic.  This needs to be fixed in the next update (sooner rather than later). 

Other than that, I LOVE my JTV.