Just a quick observation with the latest S3D 3.0 on Mac OSX 10.9.5. When you import a model within the application your STL is imported and you see it centered on the bed. But, if you import a second model, the first model disappears. If you then click the "Prepare to Print" screen button, you then see both models.
If you drag and drop multiple models from a folder on your desktop to the S3D table view, all your models are displayed as normal. The problem only appears to be with when you click the Import button within the S3D application.