Be sure you don't have any other libraries in your build path that may use a different version of OWLAPI. In my case, it was the wrong ELK version in my build path, which leads to very mysterious errors such as:
Exception in thread "main" java.lang.NoSuchMethodError: org.semanticweb.owlapi.model.PrefixManager.setPrefix(Ljava/lang/String;Ljava/lang/String;)V
See also this thread from the OWL API mailing list.
I am nervously waiting for version RC4.
Other owlapi posts
drseb ONTOLOGIES · OWLAPI