This issue is caused by the fact that the referenced fluentnhibernate is using a different version of the NHibernate, and the version that you added is not the same. NuGet re-adds the latest version of Fluentnhibernate.
or add version redirection in the configuration file, new version adds the NHibernate version for itself, oldversion the version used for Fluentnhiberbate
<configuration>
<runtime>
<assemblybinding xmlns= "Urn:schemas-microsoft-com:asm.v1" >
<dependentAssembly>
<assemblyidentity name= "NHibernate" publickeytoken= "AA95F207798DFDB4"/>
<bindingredirect oldversion= "3.0.0.2001" newversion= "3.3.1.4000"/>
</dependentAssembly>
</assemblyBinding>
</runtime>
</configuration>
The referenced NHibernate assembly version is inconsistent with the NHibernate version used by fluentnhibernate, resulting in a failure to load the file or assembly "NHibernate, version=3.0.0.2001 Error