I do have exactly the same problem.
I have Joomla 1.5.3 with Joomla 2.0 beta and JoomSEF 3.1.2.
My site has English and Japanese.
My home page is in English. So every new user will get my page in english by typing http:
www.monsite.com/
All the URLs which began by index.php are being changed and translated by JoomSEF.
But, if from one Japanese page, I click on the default item of the menus (the item which leads to the home page),
normally with just Joomfish, it would be the home page in Japanese (I mean the page will remain in Japanese); but here with JoomSEF and Joomfish, just the contents of the page are still in Japanese and the items of the menus are translated in English.
I think it is due to the fact that JoomSEF doesnt manage the URL which doesn't begin by index.php?.....
because the original URL of the homepage is just
www.mysite.com/
Do you have an idea to solve this issue.
Best.