Hello,
I'd strongly advise against putting nested lists in properties - or even using the datatype "d:any" at all if not avoidable. Your data structure would probably best be served by using composite nodes, i.e. a main node with a list of children, each maintaining a multi-value, typed property of your actual elements. This way you have cleanly separated 2nd level lists that you can aggregate in your web scripts / code.
What I'd suppose happens here is that the automatic conversion logic of Alfresco when loading properties from the database flattens your collection.
Regards
Axel