Last two versions that I'm aware of. Yes, it reproduces. Menu > Save Settings > [filename] > ... I have to change 'save as type' to 'all' and remove [.]xml from the name and it saves fine, then add the extension manually.
This bothers me as well. I thought it was normal behavior. I was going to make a feature request for a quick save hotkey or a timed autosave.
menu->save settings->choose file->okay->are you sure?->yes
I don't understand what barium said - "change 'save as type' to 'all' and remove [.]xml from the name and it saves fine" - I don't do that, I just double-click the filename and say yes to the overwrite.