After upgrading to NHibernate 3.3 and FluentNHibernate 220.127.116.117 the ICompositeUserType from https://gist.github.com/2837045 no longer generates the correct mapping. Both the *.717 and *.727 generated files are included in the gist for comparison.
I am having the same issue as well. This version of FluentNHibernate is completely unusable because of it. I have spent a couple of days trying to track it down. It seems to related to the mapping.DeepClone in GetSubclassMapping method in SubClassMap. The mapping has the correct number before it is serialised and after it does not.