There are three places where the settings can be saved.

1. Win XP and earlier versions (Vista and Win7 can also have this path if you run CE as administrator):
   C:\Program Files\CubicExplorer\
2. Vista and Win7 (replace **** with your username):
   C:\Users\****\AppData\Local\VirtualStore\Program Files\CubicExplorer
3. 64bit Vista and Win7 (replace **** with your username):
   C:\Users\****\AppData\Local\VirtualStore\Program Files (x86)\CubicExplorer

The snapshot version of CE is installed in the folder CubicExplorer_dev instead of CubicExplorer.