equivalentClass axioms

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What steps will reproduce the problem?
0. i installed the browser at http://s1.semanticscience.org:8080/browser/

1. I loaded an ontology 
http://translationalmedicineontology.googlecode.com/svn/trunk/ontology/tmo.owl

which includes an owl:imports for
http://translationalmedicineontology.googlecode.com/svn/trunk/ontology/tmo-exter
nal.owl

but when i look at the class hierarchy
http://s1.semanticscience.org:8080/browser/classes/-200689702/?session=13123156c
17-3-13123157b76

it doesn't appear like it does in protege in that there are many classes as 
subClassOf owl:Thing, when many of these are more specific subClassOf, but is 
specified in equivalentClass axioms.  This still happens even if i turn the 
hermit reasoner on.

Original issue reported on code.google.com by michel.dumontier on 13 Jul 2011 at 10:44