Hello NORIM,
What happens, if you press Reset View button on the toolbar in the Ortho view after the second orthomosaic generation run?
If you remove empty Shapes folder from the chunk's contents then you wouldn't need to press Reset View button after new orthomosaic is generated, since the Orhto view would be centered on the new mosaic automatically.
In you case the Ortho tab is not closed (since there's Shapes folder) and the view is not reset.