Many of the term names also include very long bits of mathML make visualizing the ontology (Jambalaya, OntoViz in Protege) very very difficult, as it seems to be luck which rdfs:label is used in Protege (3.4 beta). You can only choose one over the other if you set the default language to "en" for one of them. If there is some way to have a mathML annotation property (possible in OWL, but not sure about OBO) it would make visualizing the ontology much more straightforward and easier for your users. I think this is because it is chance which of the two rdfs:labels Protege chooses to display. I have emailed them asking if they know a way to force the string rather than the XML to be displayed, but haven't had a response yet. However, I'm not sure why you have two rdfs:labels. Maybe it's due to the conversion to OWL? If they are meant to be synonyms, then perhaps you should choose one, like the string, as the rdfs:label, and the mathML as a synonym.