I was also having problems with saving options. Tried changing the permissions (chmod a+rwx limewrire.props) -- no effect.

So I upgraded to 2.5 hoping the prob would be fixed.

Now I still have the same problem, but the
limewire.props file does not even exist anymore ....

The preferences that I set (like download dir) when I started the first time are saved, but nothing else. Any ideas?