Based on your description, I assume you're using Linux, which is highly problematic for spawning an external console. When you select "Open Console" on Linux, Simply Fortran uses the command "x-terminal-emulator -e <cmd>" to launch your command line. The problem in this case is that the "ls" command executes nearly instantaneously, and, when complete, the console immediately closes. On my test system, an Ubuntu 16.04 machine that's not particularly fast, I sometimes see a window flash when I run this example.
The toolbox will work great if you have a long-running process or you don't select "Open Console." For example, in your case the command could be (without "Open Console" checked):
which will open a reliable, old xterm window, display the directory listing, and end with a command prompt.
The problem is Linux's fractured state. The only reliable commands are "xterm" or "x-terminal-emulator." Launching a native, more configurable terminal like kterminal or gnome-terminal is unreliable since Simply Fortran does not (and will not) be able to determine your current desktop.
These problems simply don't exist on Windows or macOS where a terminal can be opened in a more configurable manner.
I think I will look at possibly switching to using xterm on Linux since the "x-terminal-emulator" command is so rigid and inflexible. It just doesn't provide the same configurability as our other two platforms.