I think you are right, its the front junction box that fails. I can measure the battery voltage at the wire coming from the rear JB going into the front JB, but I cannot measure anything on the other side, at the shifter connection. Shouldn't I be able to do that?
Not necessarily, as far as I remember the front JB changes everything pretty dramatically. I remember our engineer saying everything forward of the front JB was a very simple system, but once it comes out of that it was quite a bit more complicated, so obviously there are some serious changes as it passes through the JB.
You are correct in thinking that a flaw in one piece won't necessarily stop the whole system from working. You can run Di2 when it's only partially hooked up, you don't need everything to be plugged in for it to work, which is why I'd be reasonably sure the problem is in the front harness. You should stop by your LBS and see if they have one they'd let you plug in to test your bike.
Sorry, but my bet is still on that main connector just back of that front control box jb. If it was in the front ahead of that control box jb, then it would only affect the fd or rd, depending on which side is broken, since the signals from the left and right shifters are combined at the control box jb. But maybe we are agreeing and just describing things with different words. In any case, I've seen this specific symptom when that front big connector comes adrift. Usually its because the cable was installed too short, and when the handlebar is turned, it pops the connector out a bit.