I had a problem where some attachment URLs where not getting rewritten (i.e. changed from mydomain.com/wp-content/uploads/etc. to mydomain.s3.amazonaws.com/wp-content/uploads/etc.).
It seems like a common problem, judging from these other threads:
Anyway just wanted to share a fix I found: clicking the "Modify attachment URLs" button and then changing all URLs (even if you change them to the same domain) apparently forces W3TC to reprocess all attachment URLs, and it's now rewiring all of them fine.
Hope this helps somebody else!