UAC Problem
Sounds very much like a UAC problem with Windows. Ether run the program with administrative privileges, disable UAC, or run it from a location other than \Program Files\ as suggested earlier. To test, right click the main program exe and "Run as Administrator". The \Programs Files\ (& x86) have special permission requirements under UAC that can prevent portable programs from accessing the settings (as Microsoft believes that settings are NOT supposed to be saved in the Program Files folders ;-)
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