Originally Posted by davotoula

I have now carefully gone through all of my directories and files and have made sure that:

no foreign .htaccess files
no 777 directories
no 777 files
checked all my own php/html files for foreign blocks of code
rebuilt all dynamically generated content (from CMS)

Especially 777 directories seem to be dangerous so I recommend you to chmod them to 755 to stay safe.

My Movable Type installation seemed to be creating 777 directories by default so I had to change a config file to force it to create directories with 755 and files with 644.