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That happened to me big-time last month. Every site of mine got hit. Every single index.html or index.php file on my server had random lines of code inserted. It royally fucked-up a few of my sites that used link exchange programs. Hugely annoying. It happened every day for a week. I spent countless hours trying to figure out what was going on. Fixing everything over and over again was a major bitch.
When I asked my hosting company about it (Colo-Cation, the best hosting company ever) they looked into it and told me that, as k0nr4d said, it was more than likely a virus on my own machine that was causing the issue. I ran a virus scan and changed every password on my server and it hasn't happened since.
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