Unfortunately there is a walnut gall mite and a codling moth which gets into the nut at blossom time and then they can't be stored. This is the most common reason why some nuts are mouldy.
In your case you opened the nuts so the kernels were presumably healthy at that stage. So I wonder if your storage method left something to be desired? If they were moist and stored in a plastic container they would go mouldy.
Why not just store the nuts in their shells which is what the French here do (and so do we). You may get the odd one which is no good, but the majority last well into the spring.
Another thing you could do if you want shelled nuts, is to dry the kernels first and then put them in the freezer in a bag. That would stop them going mouldy though you'd need to defrost them when you wanted them.
This year here looks like being another bumper crop year for walnuts as we have a 40 foot tree covered in them. I hope you get a similar large crop that keeps well this time.