[cmd] What is the reason for the error message "System cannot find the path specified"?

There is not only 1 %SystemRoot%\System32 on Windows x64. There are 2 such directories.

The real %SystemRoot%\System32 directory is for 64-bit applications. This directory contains a 64-bit cmd.exe.

But there is also %SystemRoot%\SysWOW64 for 32-bit applications. This directory is used if a 32-bit application accesses %SystemRoot%\System32. It contains a 32-bit cmd.exe.

32-bit applications can access %SystemRoot%\System32 for 64-bit applications by using the alias %SystemRoot%\Sysnative in path.

For more details see the Microsoft documentation about File System Redirector.

So the subdirectory run was created either in %SystemRoot%\System32 for 64-bit applications and 32-bit cmd is run for which this directory does not exist because there is no subdirectory run in %SystemRoot%\SysWOW64 which is %SystemRoot%\System32 for 32-bit cmd.exe or the subdirectory run was created in %SystemRoot%\System32 for 32-bit applications and 64-bit cmd is run for which this directory does not exist because there is no subdirectory run in %SystemRoot%\System32 as this subdirectory exists only in %SystemRoot%\SysWOW64.

The following code could be used at top of the batch file in case of subdirectory run is in %SystemRoot%\System32 for 64-bit applications:

@echo off
set "SystemPath=%SystemRoot%\System32"
if not "%ProgramFiles(x86)%" == "" if exist %SystemRoot%\Sysnative\* set "SystemPath=%SystemRoot%\Sysnative"

Every console application in System32\run directory must be executed with %SystemPath% in the batch file, for example %SystemPath%\run\YourApp.exe.

How it works?

There is no environment variable ProgramFiles(x86) on Windows x86 and therefore there is really only one %SystemRoot%\System32 as defined at top.

But there is defined the environment variable ProgramFiles(x86) with a value on Windows x64. So it is additionally checked on Windows x64 if there are files in %SystemRoot%\Sysnative. In this case the batch file is processed currently by 32-bit cmd.exe and only in this case %SystemRoot%\Sysnative needs to be used at all. Otherwise %SystemRoot%\System32 can be used also on Windows x64 as when the batch file is processed by 64-bit cmd.exe, this is the directory containing the 64-bit console applications (and the subdirectory run).

Note: %SystemRoot%\Sysnative is not a directory! It is not possible to cd to %SystemRoot%\Sysnative or use if exist %SystemRoot%\Sysnative or if exist %SystemRoot%\Sysnative\. It is a special alias existing only for 32-bit executables and therefore it is necessary to check if one or more files exist on using this path by using if exist %SystemRoot%\Sysnative\cmd.exe or more general if exist %SystemRoot%\Sysnative\*.