I had the same problem, but I seem to have figured it out, at least for my site.
I set up an url alias with the system path as 'node' for all languages.
Then I added the alias /home
Whenever you reference 'home' it just points at the standard frontpage.
My problem was going from the homepage to a section in my site.
Then I would switch the language and click back to the homepage.
When I got to the homepage, despite the url reading /en (my default is /ja )the links would not include the English prefix.
This fixed it.
However this is a mobile site and I am referencing the homepage via the header image which I have point at the homepage in the page.tpl template.
English
Deutsch
Español
You don't need a homepage
I had the same problem, but I seem to have figured it out, at least for my site.
I set up an url alias with the system path as 'node' for all languages.
Then I added the alias /home
Whenever you reference 'home' it just points at the standard frontpage.
My problem was going from the homepage to a section in my site.
Then I would switch the language and click back to the homepage.
When I got to the homepage, despite the url reading /en (my default is /ja )the links would not include the English prefix.
This fixed it.
However this is a mobile site and I am referencing the homepage via the header image which I have point at the homepage in the page.tpl template.
language.'/home'; ?>"" >
/>
So it might not be for everyone.