I've had some Carnuba Wax been sat still for a long time, it had done the same thing, gone all watery and horrible, I shook it for ages, but when I opened it, it smelt like old chip fat, rancid.
As I'm a qualified Aromatherapist, I assumed the wax would have a use by date, much the same as most of the oils I use for my job.
It is probably gonna sound bizarre but I wouldnt use it on my car, even tho it's only a car!!
Hope this will help you.
Caz.