Vapor pad should have no affect on whether the carpet stinks or not.As far as over wetting the carpet,I am sure you you would not be wetting a carpet so much as to soak a carpet backing to the point of basically having a puddle on a vapor padding. Pads that would adsorb the moisture would be the ones I would worry about leaving an odor.
Since I have a great friend who owns a flooring store, a test is in order to see just how much id have to over wet a carpet to create a problem.
My though is you just ran into a freak situation, or the new carpet it self was a cause.
The JAGUAR 8.4 INDUSTRIAL SYSTEM; not your generic squirt & suck machine!