The most likely explanation is that your program is 32-bit and Explorer is 64-bit. When a 32-bit program opens files in C:\Windows\System32(which contains 64-bit DLLs), it is actually redirected to C:\Windows\SysWOW64(which contains 32-bit DLLs). The size difference you see is the difference between C:\Windows\SysWOW64\gdi32.dlland C:\Windows\System32\gdi32.dll.
For more information, see KB Article 896456 .
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