With the stand alone version of KillEmAll it doesn't run all the time, when you run it it kills running processes then allows you to take actions on those processes. You could have created IFEOs to prevent running some programs but doesn't sound like that would be the case here. You can check however using the IFEO modifier here: http://download.foolishit.com/IFEO_Modifier.zip
If there is anything listed in the "Delete an existing IFEO" section you can safely "Delete All". If there is nothing there there is something more going on with the system.
What actions did you take when you ran KillEmAll?
What prompted you to try running KillEmAll in the first place?
We may be able to narrow down more from those two answers.
Chief Operating Officer, dSupportOnline official support of Foolish IT
& long time tech friend of Nick & avid Foolish IT product user since before Foolish IT was even created!