Ok in 16.5 this 3d viewer is acting kind of wierd in particular with the Z plane.
If you create a Shape on the Package Geometry top class and enter the height parameter as a positive when you hit the 3d button to display the 3d representation of the shape it is flipped, I.E the default view is negative with respect to the Z plane. Now if you enter a negative height properity for a shape then the 3d view looks fine when creating symbols.
Here is the issue. If you use negative height parameters so your 3d part looks ok in the symbol editor when you place the part on the board and hit the 3d Button the actual visual representation of the 3d shape is negative. Seems like a bug with the Z scaling between symbol editor and pcb editor. Anyone come across this ?
Steps to reproduce would be
Create a rectangle in the symbol editor on the package gem top class, give it a min height value of 0 and a max height value of say 50, click the 3d button, you will have to pan tilt to see that the positive z plane height is negative.