The Coverings work differently for ArchiCAD 18 compared to ArchiCAD 17 tool. The new way the covering works will determine of the Door or Windows openings are detected by the coverings or not.
The recommended practice for ArchiCAD 18 would be to have the right renovation default filter before applying the covering, so please consider the following:
Open the Renovation Palette:
Command menu Window>Palettes>Renovation
– Before selecting the wall, deselect all elements
– Select “New” or “To Be Demolished” (whichever you need) to be the “Default Elements” status.
– Select the wall and attach the covering tool normally.