Try checking the user or service that is running the application pool has permission to execute the command(s) you need. It could simply be a permission problem.
I wouldn't expect anything to occur in the UI session if you are logged onto the machine at the same time though. The user running the service is only a process and is run and monitored by IIS.
You should see the process starting and ending if you open the task manager and check the option to show all processes for all users. This would be similar to running a database job and expecting to see the SSIS package open/run etc.