Using the following code in program to reason an OWLOntology takes ~3 min:

        OWLOntology MSO = ioHelper.loadOntology("MSO_unreasoned.owl");

        OWLReasonerFactory reasonerFactory = new JFactFactory();

        ReasonOperation.reason(MSO, reasonerFactory);

The same file and reasoner takes 1 min in Protege. File is attached (remove .txt extension). I have other files that take longer to reason in Protege and the time multiplication factor in code gets larger the longer in Protege it takes.
MSO_unreasoned.owl.txt