The Jag-Stang switching is as follows:
If both switches are switched on in the same direction then the pickups are in phase, if they are going in opposite directions they are out of phase. If only one switch is on then it cannot be in or out of phase. Obviously.
eg; if you slide the neck switch to the left and the bridge switch to the left, they are on in phase.
if you slide the neck switch to the right and the bridge switch to the left then they are out of phase.
There is no other explanation, there is no argument, this is not debateable. If your switching works different then it is not wired as stock.