I have several applications that are 32 bit executables and redirect to the Wow6432Node in the Registry (an example is a desktop/shell replacement called Litestep, and another called SharpEnviro). This normally wouldn't be an issue, but for example, trying to run the 'sfc /scannow' command in SharpEnviro in CMD gives an error. Navigating to 'C:\Windows\System32' in CMD and then running 'sfc /scannow' works fine. I think this happens because Registry redirection keeps causing CMD to redirect to the 32 bit version of CMD and SFC on my x64 system. Litestep has both a 32 and 64 bit version, but the x86 version cannot run 64 bit plugins, and the x64 version cannot run 32 bit plugins. The 32 bit version is more supported and has many more plugins, so I think it is what I should be using.
Are there any reasons I shouldn't do this, and is it even possible to completely disable this redirection? I plan to do this immediately on a clean install for best results, before installing any programs, drivers, etc.
I had recently found a webpage by MS on how to do this, but can't seem to locate it after searching on Google.