The option to use cracked section properties or gross section properties is specified in the Analysis Options dialog, which can be opened by clicking Analysis > Analysis Options.
This applies to concrete beams, columns, and shells.
The cracking factors are specified in Create (or Modify) > Member Properties > Cracking Factors or in Concrete Design > Cracking Factors.
Cracking factors will not be applied until “Use cracked section properties (Icr) for members and finite elements” is checked here in the Analysis Options dialog.