Steps to the problem:
>I added a remote agent, it installs and runs perfect.
>Added a capability under Executables - C:\Windows\System32\cmd.exe (to run batch scripts or executables)

>When I create a plan, I add a task under a Job, using CMD as the executable.
>I pass in the arguments as [ /c "C:\Windows\System32\notepad.exe" ]

Now when I run the plan, it launches the notepad, but it launches it minimized. I want to run some Sikuli Tests eventually, but it will be a major problem if the applications launch minimized.