Hi Danni,
As you found evidence of rootkit activity, I’d suggest running the Panda anti-rootkit scanner:
http://www.pandasoftware.com/products/antirootkit/
Run the in-depth scan which requires a reboot.
Follow this with a scan by DrWeb CureIT!
http://download.drweb.com/drweb+cureit/
If you can’t run this program, rename it and see if that allows you to run it.
Also, try the F-Secure online scanner:
http://support.f-secure.com/enu/home/ols.shtml