there's no need for secrecy because there's hundreds of sites that will inform you about Cross site scripting or other ways to attack a website.
Ioi:
Since I have adblock plus installed since ever, I assume it's not the ads. (I never see any flash on this site because its blocked.) Nevertheless I got two warnings today from my Work-PC's Norton antivirus (got linux at home, yay). To be sure: deactivate all the ads for a day or two and watch if it changes anything.
It's true that somebody could have got your PW through keylogger or else. If you login using ftp note that this is not secured at all. If you have the possibility, only allow file changes on your server through sftp or scp. (and of course change your pw and check your private pc thoroughly)
You said the header file is being modified by the hacker. If your webserver is a linux machine, check yourself or, if you can't, let your host provider check which users/groups have write permissions on the file. If the web server user is allowed to write that file, then your PHP frontend could have a security issue which needs to be fixed.
If not, then the hacker probably has your password and logs in with your account. Or he's got another way to log into your webserver.
It's not an easy task to find out how a site is getting hacked, but if you try out a lot of different things I think you will be successful.
PS: Just another thought. If you can, edit your php.ini to the highest possible security settings. If not, you can override the settings manually in the php code. Check out http://www.phpfreaks.com/tutorials/10/0.php







