Starting in macOS Mojave (Version 10.14), permission must be given to any program that tries to access your microphone. This includes any audio interface input that is to be used with SoundCheck. When the prompt appears, "OK" must be selected to use the input device.
If the prompt is missed, permissions can be enabled in System Preferences > Security & Privacy > Privacy > Microphone. Enable the checkboxes next to SoundCheck to allow access to the inputs.
For more information, see the following article from Apple: