This is most likely caused by the file system redirector in Windows. NXLog on Windows is a 32 bit binary so the system32 folder is mapped to a different path.
But what about 32-bit applications that have the system path hard coded and is running in a 64-bit Windows? How can they find the new SysWOW64 folder without changes in the program code, you might think. The answer is that the emulator redirects calls to System32 folder to the SysWOW64 folder transparently so even if the folder is hard coded to the System32 folder (like C:\Windows\System32), the emulator will make sure that the SysWOW64 folder is used instead. So same source code, that contains a path with the System32 folder included, can be compiled to both 32-bit and 64-bit program code without any changes.