The problem can be easily reproduced by taking any concept description which is not satisfiable and asking for its equivalent classes.

The expected result should be a set having bottom (e.g. OWL:Nothing) as its only element, but the output is the empty set instead.

The described issue is present in the latest version of the reasoner (v1.3.0). The version I previously used was 1.2.3 which seems to be unaffected.

Note that if we ask for the ancestor classes of the same (unsatisfiable) concept description, all of the classes in the ontology (plus OWL:Thing) are in the output as expected.

This problem should be fixed in the current SVN (post-1.5.0)