This is a concern to many of us Hosters and after some in-depth research of my own, it would seem the most likely cause is that your personal computer is infected
. Strange as that may sound, hackers are using a variation of Trojans to infect personal computers and then use your own FTP login information, to change the Index page and/or other targeted pages on your own site.
Please use your Anti-virus program to check your personal computer and advise if anything was found -- including links to Web sites with more information specific to the Virus/Trojan found, like this article
. I can only presume (hope) that you have an Anti-virus program but if you don't, you can have computer checked for viruses for free -- using the free HouseCall from TrendMicro
. They are a very respected company when dealing with Virus related problems. You can feel secure in using their HouseCall program to access/clean your computer.