Is this fixed?
The problem sometimes originates from a trojan on your PC, that will use your ftp login to upload modified and infected files.
Usually they add encoded/encrypted javascript that connects to the malware sites infecting your visitors.
It is just one line usually loading an external javascript.
The only way to get rid of this is to get your PC clean first.
You also better change your ftp password ASAP because that has been compromised.
And if your ftp program has the option to password protect the logins/site manager then better do so.
After your PC is clean, and certified to be clean, you should go through all your site's file and remove the javascript manually.
Pretty tedious. Just be careful that you do this while offline if you want to check the pages in a browser.
The javascript itself is harmless, I mean it is not a trojan or anything.
It just downloads trojans from other sources. If you're offline it can't.
So you can just remove it.
Just look for any javascript you didn't add yourself and delete it.
Just reuploading your files is not gonna solve it, you have to check each and every one of them.
It might be a good idea to talk to your host and ask if they have been hacked recently, that's another way in which this spreads.
I didn't see your site so I have no idea what it is, html, php or whatever. If you're running Wordpress or any other CMS get the latest update before reinstalling.
And be careful with what advertising services you use, a lot gets spread via those via javascript or via flash.
Some of them promise a lot and deliver even more!
Edited by xmephistox, 07 June 2010 - 11:54 PM.