Some informations that may help:
WP 3.5
Amazon S3
W3TC 0.9.3
Enabled: CDN, browser cache and object cache
The unsuccessful file transfers list is always empty (seriously, I've never see one file listed thered). So there is nothing to clean.
And I did upload (again) every content available (media library, wp-includes, theme files and custom files). Actually, when I try to access some file directly at CDN, it works fine, like: http://cdnprev.s3.amazonaws.com/wp-content/uploads/2013/06/dinheiro-100x76.jpg .
So, it's just the rewritable stuff that it doesn't work anymore and I don't know why.
Today by morning the plugin was working fine. The only change I've made was in footer.php (some facebook + google plus javascript), in custom.css and in single.php (like, tweet and +1 buttons).
I've already tried to deactivate and activate W3TC, but nothing changed.
And finally, when I try to send a bug report, it shows that I have no permissions even though I have super admin flag.
(sorry for the bad english, brazilian here \o/ )