Hey Eli,
Love the plugin. I recently let my hosting account become seriously infected (it spread across all my sites). Your plugin did a great job of finding and removing the files... but my problem persists.
The main symptom is more annoying then anything else. Something is adding a series of scripts to the end <head> section and I can't work out what it is.
Have a look on both these sites:
http://heartmen.net/
http://littlebootcampbooks.com/
If you don't see the scripts right away, try clicking on another page. You'll know it's loading those scripts when the page takes 30+ seconds to load.
Kyle