In Windows 7, for Encore CS6, the file is in the path:
C:\Users\[User Name]\AppData\Roaming\Adobe\Adobe Encore\6.0
The file is AppPreferences.xml
Holding Ctrl and Shift down while opening Encore deletes that file. Encore does not open during that process. When you then open Encore, it creates a new preferences file.
The file name (and path) appears to be the same (except for Encore version number in the path) for 5.0, 5.1, and 6.0.