Please have a look at the "Directories" in the "Settings" when you run Spybot - Search & Destroy in "Advanced Mode".
There you can add additional harddisks or folders.
You can also use the command line parameter allhives.
/allhives
Scans all windows installations on your system, even inactive ones.
Example: "C:\Program Files\Spybot - Search & Destroy\SpybotSD.exe" /allhives Take a look at our FAQ entry 30.
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