Windows ALWAYS "uses CWD as Root". Here is the one and only place in KoLmafia source where that definition is examined:
Code:
public static final File BASE_LOCATION = new File( System.getProperty( "user.dir" ) ).getAbsoluteFile();
public static final File HOME_LOCATION = new File( System.getProperty( "user.home" ) ).getAbsoluteFile();
public static final File ROOT_LOCATION =
Boolean.getBoolean( "useCWDasROOT" ) ?
UtilityConstants.BASE_LOCATION :
UtilityConstants.USE_OSX_STYLE_DIRECTORIES ?
new File( UtilityConstants.HOME_LOCATION, "Library/Application Support/KoLmafia" ) :
UtilityConstants.USE_LINUX_STYLE_DIRECTORIES ?
new File( UtilityConstants.HOME_LOCATION, ".kolmafia" ) :
UtilityConstants.BASE_LOCATION;
As you can see, for non-OSX, Non-Linux systems, the root directory is BASE_LOCATION - which is exactly what the Java define forces.
What exactly is your Current Working Directory when you execute KoLmafia off a flash drive from OS X?