The issue seems to be caused by initializing the CLI GUI with a valid parameter node and an invalid scene. See details below.

• MRMLCommandLineModuleNodeSelector->setMRMLScene is called, it finds a good node in the scene, so selects it
• currentNodeChanged event, which calls
• qSlicerCLIModuleWidget::setCurrentCommandLineModuleNode, which triggers
• qMRMLNodeComboBox::setCurrentNodeID methods, but the scene is not set yet
• qMRMLNodeComboBox::setScene

void qMRMLNodeComboBox::setCurrentNodeID(const QString& nodeID)

QModelIndexList indexes = d->indexesFromMRMLNodeID(nodeID);
if (indexes.size() == 0)
=> it shouldn’t be 0!!! – the index is empty somehow

The problem is that the MRMLscene is set after setupui?

qSlicerAbstractModuleRepresentation* qSlicerAbstractCoreModule::createNewWidgetRepresentation()
newWidgetRepresentation = this->createWidgetRepresentation();
...
newWidgetRepresentation->setModule(this);
...
newWidgetRepresentation->setMRMLScene(this->mrmlScene());

QWidget* qSlicerCLIModuleUIHelperPrivate::createImageTagWidget(const ModuleParameter& moduleParameter)
widget->setMRMLScene(this->CLIModuleWidget->mrmlScene()); <= scene is NULL

Fixed in https://github.com/Slicer/Slicer/commit/ed8673edd99afc9718d5e6f2198f7ed08f36cc9b