Where in the world could the ghost voltage be coming from?
That is what we are trying to figure out.
Right now we are not trying to figure how we are trying to figure
where it got there.
When you know where you can find out how.
If I understand your last post correctly, you turn off everything in the main panel except the feed to the sub-panel. In the sub-panel you turned off everything except #13 (black). Yet you have 46 volts between #3 (red) and neutral.
That means the only source of the voltage on #3 (red) is #13 (black) between the sub-panel and the junction box, or one of the cables between the main panel and the sub-panel, or the service lines into the main panel. I think we can eliminate the main lines into the house. Lets see if we can eliminate the cables between main panel and the sub-panel. In the main panel, if you can turn off the leg that feeds the upper half of the sub-panel where #3 (red) is. Check the voltages at the junction box. Then repeat turn off the cable to the lower half of the sub=panel, turn off #13 (black) and turn on #3 (red) Check your voltages. If you have a double breaker in the main panel and can't turn off the legs independently, Just disconnect the wire from the breaker. I wouldn't expect to see any differences in the reading, but we are desperate here.
Another way would be to run a temporary 2-wire cable, doesn't matter what size, between the main panel and the sub-panel.
Now there is no point in doing any of this if the cable between the main and the sub-panel and the cable between the sub-panel and the junction box are physically separated such that there is no possibility of them coming in contact with each other.
After doing this or not doing this you should be able to say with certainty that the that the voltage on the red is coming from the black between the sub-panel and the junction box. You have voltage on a neutral, but not with everything else in the house turned off. Therefore the voltage on the red cannot be coming from the white.
Two things to keep in mind, although I don't know what they mean in this little adventure right now.
You could have a connection between two wires that is so poor or bad that almost no current flows between the two wires. A voltage check would show voltage on the second wire. It might show full voltage or it might show a reduced voltage, all depending on the connection and the resistance of the connection. An example of that might be that you are working with stranded wire and one strand sticks out and comes in contact with another wire. A voltage check would show voltage but there is almost no current flow (amperage).
Second thing to remember is that when you do a voltage check you are measuring the difference in voltage between two conductors, not how much voltage is on either wire. When you do a voltage check between hot and neutral you assume that the neutral is properly grounded. Therefore you reading is an accurate reading of the voltage on the hot. If the neutral is not properly grounded and the connection has a lot of resistance, your reading will not be accurate with respect actual voltage on the hot. You could also have a connection between the black and the red but the connection is so poor or so weak that there is a 46 volt drop across the connection. In other words you have 120 volts on the black and 74 volts on the red. Your meter would show a 46 volt difference. How could you have such a connection? You could have cracked insulation and have moisture making the connection. Remember this connection is so weak that no or almost no amperage is passing.
How is the weather there? Having any rain, any snow on the roof?
You may have to set up that separate ground to get accurate voltage measurements.
God my fingers are tired, I am not very proficient at the keyboard and I am sure that this is more than you ever wanted to know..