Looks like your site somewhere has some mailicous code inside it. It could be in one of the file but also in the DB.
First of all (I hope you don't have modded a lot of files, download the full v6.01.16 package from this server and upload it again to your FTP, making sure you overwrite everything on the FTP.
Check the files and folder on the FTP to be correctly CHMODed.
I was thinking.. should be maybe good to know if all the hacked sites are hosted on the same host, as I see that some of them are on servage (me to :( )
I mean, the sites hosted on Servage was hacked, but the sites (php-fusion) hosted on other host was not.