If I'm following what you have going on I would go into Expert mode, right click model, choose model alignment, and select plateless model with extra dies. when that's done, right click and select, i can't remember the exact name but the option to create model and follow those steps. Then, you should have the model and the pontics in place (if you set up as pontics?) and make sure you do one arch at a time so only the upper model and then only the designed teeth and Nothing Else! Right click Save and Export scene to mesh. I use this when doing most of my diagnostic wax ups. The other option is when in the model alignment mode, select the diagnost model. Then when you right click and select the create model you need to make sure the box next to include pontics is selected.
The important thing will be in how you set the case up in exo Database though. I think they all need to be pontics.