If your dedicated server has suffered a mass defacement (def. most of the websites hosted in your server has been defaced), checking/scanning and removing the malware or changing password methods will not resolve the issue permanently. This is because the kernel and server system files have been compromised.

SOLUTION:
1.  Migrate all hosting to a new server with a cloud Linux kernel
2.  In the new server disable Perl, centralize PHP with PHP-disable function.