I have been running into this when I am saving or updating settings on my wordpress installation. Where I will be rocking and rolling updating pages etc, then when I hit save/update, it will loose the domain and will 404 error. The address bar will then read:
If I simple go to the address bar and type in the url.com it saves and works again.
I am on a mosso server, which has hindered some things in the past, but I wanted to check here first.