What I recommend is to install a script that checks every 15 minutes for changes in your files, if something was found different, send a report by email.

By doing this I can then know if I got infected. The next step is use another perl script to remove the iframe tag from my php files.

For all these scripts check my article (in portuguese)

Any questions, just ask. Good Luck!

Also you need some basic steps to protect your computer like, using Yahoo anti-spy ware to scan after every browsing session. Plus improve on passwords e.g. use ~!@#$%^% before password and after password as well instead of using alphabets use numerals in their place e.g. in place of “E” use “3″ or “0″ use “o” etc.

If you have a host who’s sensitive to attacks and has put the right systems on track you will have more of this. I used to experience the same but when I changed my web hosting I’ve never had to worry about Hack attacks. See if you can switch to more reliable hosting.

I would recommend to you a site/domain monitoring tool to notify you (in real time) if your site is ever modified or added to a malware blacklist. free and simple: http://sucuri.net