On a Windows system, the commands function instantiates a 32-bit command process, so any command with 64-bit dependencies may not be recognized or run properly. There are numerous reasons, but in many cases it may be triggered by .net Classes, Snapins, Modules, or even COM Objects that are 64-bit dependent.
To force a 64-bit system to launch a 64-bit command process via JumpCloud Commands, leverage the Sysnative virtual directory to call either cmd.exe or Powershell.exe directly. There is additional information on MSDN regarding the Windows file system redirector.
An example template for running a 64-bit PowerShell command.
An example template for running a multiline 64-bit PowerShell command.
%windir%\sysnative\cmd.exe /C your_command
%windir%\sysnative\cmd.exe /C wbadmin enable backup