It leaves a config file in C:\Users\%username%\AppData\Roaming\Macromedia\Flash Player\#SharedObjects\ULU4AQQF\localhost\PortableApps\WorldClockPortable\App\WorldClock\worldclock-flash-clocks.exe\ .
The name of this file is WorldMapColorDataEx.sol .
The file is not saved , and everytime you move to a new computer ( or a cleaning program cleans cookies) it resets to defaults.
I am on a Win 7 computer.