Suppressing prompts may cause lockups if no default action is available for the event in question, or if the prompt was produced by an error. When running the TE in this mode using Windows scheduler from a different user account, the TE will not be accessible from its COM or GUI interface and can only be unloaded via the Task Manager.
The best way to avoid prompts is to properly configure the TE ahead of time to cover all possible prompt scenarios, such as overwrite conditions, or SSL server certificate acceptance dialogs. For example, set your overwrite actions under CuteFTP's global settings to Always Overwrite to avoid any overwrite prompts, or pre-define various rules to cover various overwrite scenarios.  You can then export those rules as registry entries and import them onto the target computer.

You can also tell the TE to auto-accept SSL or SSH certificates using the AutoCloseMethod parameter of the Option method. Also refer to the following trouble shooting topic regarding running the TE while not logged in.