Well, you’ve already deleted them, from what I understand, however they malware came back. Which is why I’d want you to check the PC for malware.
But, just deleting them will not remove the warning, so you may actually just have to request a review
Here’s the “how to”:
Malware & Hacked Sites FAQ – Image of the Dashboard & Request a Review Link
http://sites.google.com/site/webmasterhelpforum/en/faq-malware-and-hacked-sites
*Add the site to Google Webmaster Tools (if it not already there)
*Verify ownership of the site (if you have not already done so)
*Click the site so you can see the Dashboard for that site
*Click on [ More Details ] from the red malware warning bar
*Click on “Request a Review” and complete the form
*Wait a few hours to a day or so for the warning to be removed from the search results (IF the site is clean)
*Check your messages in Google Webmaster Tools for messages related to the status of your review
Google webmaster tool is here:
http://www.google.com/webmasters/tools/
Sounds like as if someone else uploads the files right after you have deleted them.
Run a scan for malware and virus, change your password and try to delete again. If this is a compromised password it should prevent reuploading.
When you have deleted the files, make sure to check with your FTP/Cpanel that the files are gone.
