Regarding the last message: I was able to save the ontology. I minimized the Protege window and then restored it and while it still looked like a total mess after the restore when I clicked on the File menu I did get a drop down menu and was able to select save. Also, I did a cntl-s earlier and one of those things worked.
Unfortunately I can't send the ontology, that created the error. I don't have permission from the client yet to make it public. I think we will get it eventually but it's a big bureaucratic organization so want to err on the side of caution.
Also, I'm not sure the ontology matters that much. I've seen similar behavior in other ontologies since I started using the latest version and it seems rather unpredictable. What caused the error that disrupted the screen was having an ontology with a data property where one individual had two values. Then declaring that property to be functional caused (naturally) an inconsistency but also it messed up the screen.
I got the same problem when I tried to test my ontology's consistency with a
reasoner. I was able to save it as well, but I think that it also occurred
because of an inconsistency after I ran the reasoner.