The issue is folder redirection, If a 32 bit program attempts to access the %windir%\System32
folder it will be invisibly redirected to the %windir%\SysWOW64
directory, this is for 32/64 bit application compatibility.
All the files in System32 are 64 bit, however if a program was incorrectly written they may have hardcoded the System32 in to their program when looking for a DLL. To prevent random program crashes from incorrectly written programs Microsoft does that redirect.
If you need to access the System32 folder and not the SysWOW64 folder navigate to the "hidden" folder %windir%\sysnative
which will take you to the "real" System32
folder and you can browse the folder like normal.