Yes, there are some preferences that get saved in locations that depend on the operating system (on the Mac, in
~/Library/Preferences/com.apple.java.util.prefs.plist, but that's not a file meant for user editing).
I'm not sure, though, what is causing it to switch back to 3. I did a quick test on my Mac and if I switch the mode (between 1 and 3 in the Preferences->Spectra GUI) and quit and restart it does seem to remember that setting when I restart.