The Command Prompt User Interface displays to you because you execute commands interactively. What happens is your application executes its command inside an IIS Express background session because of which everything runs without displaying any output. Running commands through your C# application under IIS Express produces different working directories compared to your command-line operations which affects file path references.
The system behavior of UiPath depends strongly on whether the Assistant stays connected to the internet. When users disconnect their internet after their robot goes online their processes tend to execute without issues. So, try these:
The observed behavior where your command executes properly in CMD represents a difference between these environments since C# fails to display the visible output.