All basses vary slightly - even two from the same manufacturer made with the same materials, so I wouldn't be too surprised at variations.
One point though, aren't the pickups in the VM series "Duncan Designed" rather than "proper" SDs? Still decent units, but not quite the same quality as the real thing.
There may also be differences in the circuitry (potentiometers and capacitors for example) that might explain some of the differences you have noticed. String brands and ages can make a difference, yes - but not usually as much as pickup height.
Lots to consider!