I think I know what you are talking about, I has a similar set up in my house and here's what I found. The power cable from the breaker box ran directly to the light fixture. From there a 14/2 wire ran to my first switch, the white was hot and the black was the return hot, in other words if I took these 2 wires and connected them together the light would come on. I had to replace this wire with a 14/3 wire, which supplied my missing neutral and cured all my problems. You said some of the box's are multiganged, If any of the other wires are on the same breaker and have a neutral this would solve your problems.