"monkeylogic_cfg2.mat" is the default configuration file that is automatically loaded when NIMH ML starts up. To create it, click on the [Save settings] button before loading any conditions/userloop file. Make any necessary change in the settings before saving.
All other configuration files associated with tasks ("taskname_cfg2.mat") are created by copying the currently loaded configuration. Therefore, the default settings in monkeylogic_cfg2.mat propagate to other configuration files when the task is executed for the first time.
monkeylogic_cfg2.mat is created in the Windows AppData directory and not deleted when NIMH ML is uninstalled. It is a convenient way to keep system-dependent hardware settings such as DAQ I/O assignments.