Hi,
The W3 Total Cache caches the files, it needs to be cleared from time to time. try clearing it if you can login to wp-admin.
It is in top menu Performance=?Empty Caches.
Else you can also clear it from /root/tmp/pear/cache if you have root access or clear it from the place on server where cache is stored.
had a similar issue for my website and resolved it this way.
thanks
Anu