I run a scan on my external HD and it completes. I run a scan on my internal HD and it crashes about half way. Any ideas why?
There could be a couple of causes related to the issue you're having:
The software is bugged and doesn't work as it should. Sometime along the scan is causing the crash.
A file is in use and is not available to access it, because of that it crashes and the code of the app is causing this.
You're not launching it as Administrator to give it access to the System partition for exclusive scanning.