What console message are you seeing that mentions anything about keyboard keys, when you stop all commands?
Stopping all commands using the "Stop All Commands Hotkey", or the UI buttons on the main window and the "Add/Edit a Profile" window, stops *running* commands; It does not prevent commands from being triggered.
If you want to disable keyboard shortcuts, you need to click the button on the main window (the one that looks like a keyboard) so a red symbol is displayed over it, or use the "Disable Hotkeys" action in a command.