I dunno about the mapping plugin, but when I come across this situation I usually try to make sure the service passes something that has all the possible fields, even if they're null. Barring that possibility I have sometimes manually "massaged" the data before calling the mapper, or created a dummy shell object that has all the possible properties set to null (or [] in the case of arrays) -- then use $.extend(dummy, real) to create something .fromJS() can work with. You'd have to iterate through the array with that pattern, but that's my $.02 anyway.
Would like to hear cleaner solutions myself too though.
var defaultCollectionItem = { alpha: null, beta: null, zappa: null };
$.each( incomingUnmappedItems, function(i, item) {