celgins - 4:58 pm on Mar 15, 2010 (gmt 0)
You say that those incoming links were valid and pointed to index.html. Can you clarify? Are those inbound links incorrectly linking to your homepage as "index.html" or do they link to the the canonical '/' as you intended?
Sorry for not clarifying. My situation doesn't involve sites linking correctly to '/', but WMT showing 404s for "index.html".
I had external incoming links to "index.html"--which were valid. Meaning, hundreds of external incoming links were pointing to: www.example.com/index.html. Since some of those site owners are unresponsive to removing the "index.html," I simply 301 "/index.html" to '/'.
I don't think I've seen a situation where an external incoming link points to the canonical, but WMT shows 404s for "index.html." Not sure if that's an issue with Googlebot or not.