After much struggle , I finally found a workaround: the issue disappears when mappings in hibernate.cfg.xml are ordered from base class to subclass:

<!-- "Right" way -->
<mapping resource="BaseClass.hbm.xml" />
<mapping resource="SubClass.hbm.xml" />

<class-cache class="com.example.BaseClass"/>
<collection-cache collection="com.example.SubClass.items"/>

<!-- "Wrong" way -->
<mapping resource="SubClass.hbm.xml" />
<mapping resource="BaseClass.hbm.xml" />

<class-cache class="com.example.BaseClass"/>
<collection-cache collection="com.example.SubClass.items"/>

Tested with hibernate-4.1.3.Final

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