You may want to check your PC for malware/viruses. It may not be your site that's being hacked. It could be that some malware on your PC is adding the iframes to your html files.

A coworker sent me an html file to upload onto a website. After uploading the html file, we found that there were iframes linking to another site. At first, I was worried that someone had hacked into our site. When I checked the html file that was sent to me by email, I realized that the html file had the iframes in it in the email...before I uploaded it. We later found out that his PC was infected with malware/viruses.

So, check the html files on your PC... the iframes may have been there before you uploaded it onto your webserver.