For the Scene document, do all your your layers have the same projection and coordinate system? It seems since you have it as being much greater that the units are still off. I would confirm that values are as expected (feet in xy and feet in z). There is a bug report out there, but it mentions that the meters selection is actually measuring feet, not the inverse. For specific help, I recommend opening a Support Incident to test with your data. I do not think the absence of a custom vertical datum is causing the issue.