I've had a look for anyone experiencing the same issue but to no avail.
I am currently working on a Wordpress site that previously did not have permalinks, so have added these (i.e. to change the URLS from ?p=123 to /about/the-company etc.) in the standard way but I've ended up with the homepage displaying a 404 error.
All of the other pages work fine bar the home page.
I have since tried deactivating it though now end up with the error still occurring. It seems to be a bit temperamental; in some browsers it works but others it doesn't.
The issue can be seen at: http://www.walkerpoolenixon.com/wordpress/
Thanks in advance!