Index page not updating the content after i manually rewrite(update) my articles

My Index page is not updating the content after i manually rewrite(update) my articles. They are ok shown under the single.php, updated, but on the index remains the old content.
I use the w3 total cache plugin. I tried disabling it, after i tried enabling and emptying all the caches, and disabling again.
Any ideas?

Files need to be updated. Some codes may be tweaked or file may be missing.

Don’t know how exactly how to update, i use the latest version of wordpress with wp-clear theme: The site is articlespedia.org

I am concerning about the manual update process with FTP, there may be some files missing or you made made any changes to the code. You can update in dashboard.

The single changes that i made to the code is adding a div id =shadow" for that shadw 3d effect. It also happens on another blog of mine: makemoneyonlinesafe.com.
Regarding the files i don’t see any missing, i have also tested with the non modified version of wp-clear and same thing.