I've never done a search on MSN for our website until today.
I found that our main page does not appear in a search on our organization's name. Yet many links to our site (including our own subpages) do appear. We are ranked very well in Google, so it seems to be something that MSN doesn't like about the main page of our site.
It might be linked to Inktomi. Sites are being removed and put back at random and MSN seems to lag. However, one of my customer's sites still has not returned to MSN after returning to Inktomi days earlier.