While looping through the item.Fields collection for a cloned item only the Sitecore standard fields showed up.

After quite a bit of googling I finally found this:

http://sitecoreblog.alexshyba.com/2009/01/friday-gotcha-sitecoredataitemsitemfiel.html

Turns out you need to call Fields.ReadAll() to get a complete collection of fields and values for the Item.