Generally odd. Yes, the upside down position of the plate, the balance before the volume (I guess that is a choice - I would expect it like KiOgons picture), the fact the tone control isn't actually wired to the circuit, but jus relies on the fact you are putting it on a metal plate, ok, it probably works (until you change the plate to plastic) but seems very bad form. I would certainly want a wire there.
On to your diagram, as you say it is hard to see because the wires are always in the way in photos, but from your description it sounds like one side is either shorted or backwards.
Do you have a meter to check that nothing is shorted out, and that the pickup inputs are only shorted to ground at full travel?
Just for clarity, on that dual pot at the top you have the volume pot at the top, one of the inputs (cant see what) in the middle, and a wire that connects to the green wire at the bottom, and on the bottom row, you have that green earth wire at the top, the other input in the middle and and output to the volume at the bottom, is that correct?