Removing the random tree initialisers from the XML (the fragment below) seems to fix the problem.
<init id="RandomTree.t:MitochondrialTree" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:MitochondrialTree" taxa="@Subset1">
<populationModel id="ConstantPopulation0.t:MitochondrialTree" spec="ConstantPopulation">
<parameter id="randomPopSize.t:MitochondrialTree" spec="parameter.RealParameter" name="popSize">1.0</parameter>
</populationModel>
</init>
<init id="RandomTree.t:NuclearTree" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:NuclearTree" taxa="@Subset2">
<populationModel id="ConstantPopulation0.t:NuclearTree" spec="ConstantPopulation">
<parameter id="randomPopSize.t:NuclearTree" spec="parameter.RealParameter" name="popSize">1.0</parameter>
</populationModel>
</init>