@brandonzundel,
Yes fair enough, but since the site has been hacked it can also mean there could be multiple places in the file system where obfuscated code is hiding.
@Joel Jerushan,
I still recommend doing a thorough clean job and then turning on the file change detection scanner in the aiowps plugin and maybe setting the file check frequency to once every 24hours. This way you can at least be notified of any file changes or additions.