In Microstation 8 views can be defined differently. So if you change off some level in View 2 and create an I–Model they are switch off in view2. However, settings are saved for the I-model, If you open the I-model in navigator it will be referenced in an empty drawing as name overlay.dgn. Here it could be that another view is shown as active and here the level are not switch off.
Please check the view numbers and open the same view in Navigator. ( KEYIN : “view off (on) NUMBER”
Regards
Dinesh Solanki