I have WP 3.01 running a website using Atahualpa with Buddypress on a linux host. Having been unsuccessful trying to login from an Xperia X10 phone with WordPress Android I checked Settings-Writing to make sure that XML-RPC was enabled.
It wasn't enabled so I set the checkbox and saved. On saving I was taken out of Settings-Writings to a 404 screen. Opening Settinsg-Writing again I see that the enabling checkbox is not set.
xmlrpc.php is however present in my root folder /public_html/ along with index.php and wp-config.php etc. Permissions are set at 644 and I have tried 666 with no luck. NOTE: There is no problem setting the adjacent Atom protocol.
I have noted that there is a different version of xmlrpc.php in one of the buddypress folders.