This often happens when you have a field that is NULL and it is mapped to a property that can't be null (such as int, DateTime, etc.). When such a field is loaded the property is initalized to its default value (which is not null) and this default value is then saved, that's why the version is incremented.
The solution is usually to use Nullables from the NHibernateContrib package for such properties.
Of course the problem may be somewhere else entirely, so please provide more details (your mappings, your classes, your code) if I guessed wrong.
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