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Differences running a program from C:\Windows vs. C:\Windows\system32

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http://serverfault.com – Calling a program in windows prompt by absolute path from C:\Windows directory is working, but calling this program from C:\Windows\System32 gives me errors. C:\Windows>D:\pathtoexe\program.exe --> OK C:\Windows\System32>D:\pathtoexe\myprogram.exe --> Terminates without doing it's task The program reads a configuration file from the current directory. The configuration file exists in both (Windows and System32) directories. If I delete the file from the Windows directory then calling the program from the Windows directory terminates with the same error as if I call it from the System (HowTos)