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This sounds exactly like the IFRAME hacks that have been discussed on this forum. Your computer gets infected with a trojan when viewing a hacked page (and you download something?). The trojan transmits your FTP passwords back to the hacker whenever you use FileZilla or other FTP client. The hacker then uses a network of infected computers to modify the web pages to plant more IFRAME hacks...
Sallen812, changing your FTP passwords will solve the problem, but only if you are 100% sure that your computer is virus free.
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