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UML2MOF does not preserve the value of the "isNavigable" attribute for the associations. It sets all the "isNavigable" attributes to true in the MOF XMI file for all the associations, without checking the original value in the UML XMI file.
This is not a bug. It conforms to the UML Profile for MOF at http://mdr.netbeans.org/uml2mof/profile.html - navigability of associations in the model is used to decide which ends should be exposed by a reference if the org.omg.uml2mof.hasImplicitReferences tagvalue is not set to false on a package representing the metamodel.