If this is any help.... I had what sounds to be the same problem with my JTV69. The D string was much quieter than the rest, nothing had changed, one day it was ok the next not. I'd not been near workbench for some time but connected up anyway to check the string levels. All ok.
So, after reading this and another thread, I cleaned the saddle with a small amount of contact cleaner and an old toothbrush.
I did also reflash the firmware but I'm sure it was the cleaning that did the trick.
I always clean my guitars down after playing/gigging but I have added 'nut sauce' to the saddles (a really small amount) but obviously this has contributed to the problem.
It wasn't immediate but after a few minutes gently cleaning, the D string came back to life.
Touch wood, all is good with it at the moment.
