When you book a record via Standard Entry and parameter Group is set to Yes, the System does not feed field Intercompany (CT2_INTERC). This field used by routine Intercompany is automatically fed when Standard Entry is configured with field Intercompany (CT5_INTERC) = Yes.
This behavior is a rule of the System, because an accounting grouping may contain various Standard Entries defined by the module of origin, with specific configurations, with the Intercompany rule active or not.
This is why the Intercompany process does not consider the records grouped, as the routine considers transactions already generated and not the Standard Entry configuration.