Altium - Variation components wrongly displayed in 3d mode
I came across the solution for this problem only now. If you go to Project -> Component Links and there are component not properlly linked between schematics and board, the 3D view will not sho these correctly. So on the refered window, if there are any components not linked, match them with the right arrow and perform update" on the bottom. Afterwards the 3D vire will show the correct models for each variant.