Do you link to "/" or to "/index.html" within your site?
I always link to the domain name only for the index page (http://www.domain.com/)
But it lasted two weeks? ouch!
Just over 3 weeks, but at least it's back.
The sitelinks haven't come back yet and now I have the top 3 positions with the same site (the 2nd and 3rd aren't indented either which is odd) so I expect it to change a bit more before it (hopefully) settles.