I've updated from 2.0.2 to 2.1.2 recently and have the following problem.
When I try to add extra RPC calls through "Update Services" on the Writing Options page, I sometimes get a 404, but this only seems to happen if the URI has a . in the name, ie if it points to a specific file rather than a directory, eg:
I then wrote a post, describing the problem at http://nerd.steveferson.com/2007/03/16/wordpress-problems-updating-settings/
And got a 404 when I included one of the same URLs. Being a novice at this I can only assume WordPress automatically tries to PingBack any URLs included in the entry. There doesn't seem to be a problem with ordinary links though, as I had no problem linking to a web page (.cfm) and a PDF (.pdf) in other posts.
Any ideas what's happening?