You might also grep the preferences file in that folder; entries in preferences override those in lyxrc.defaults.
If that also looks reasonable, you might rename the entire .lyx directory to something else (for safekeeping) and then restart LyX. It should create a new .lyx directory. I've seen reports of odd or inexplicable problems that persisted until the user directory was regenerated (although I think those were mainly if not exclusively on Windows). /Paul
