When I record in Captivate 8, the custom theme slide I use is always on top of the application background I recorded. The only way I can record software simulations currently is to record them in a new project and then copy and paste the application over a slide in the target project. Pasting as background also puts the application under the slide theme. I've used this same theme in Cap 7 and never had this issue.
I had this same issue. I was able to get around it by going to the Master Slide View on the target project, selecting the Blank slide, and clicking the trash can next to "Add Project Background." I also unchecked "Show Master Slide Objects." Now pasted simulations show up fine.
Software simulations are recorded using the Blank Master slide always. I warned several times on this forum not to delete or edit that Blank master slide for that reason. Normally it should be totally blank.