Based on the prints you referred to, it's indeed the opacities that cause the different visualization. Unfortunately the current VTK rendering doesn't do a very good job when showing models with various opacities. The change of opacities most probably happens due to automatically calculating them based on containment. This is a feature that allows the user to see all the loaded segments, because in many cases there is a "body" segment that is outside everything else, and if it's opaque, then no other segment is visible unless manually tweaking the opacities (frequently this is even more complex, as there could be a brain segment, inside that a planning target volume, and inside that the tumor).
This is where this happens: https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.cxx#L290

What could solve your problem:

1. Waiting for OpenGL 2.0. Several people are working on that, and should be coming soon
2. Adding an option to Application Settings to disable this feature
3. Writing a python script that sets all opacities to 1

Thanks for looking into this.

Can't the opacity be saved in the nrrd, like the color? Otherwise, I think it would be useful to have this in the settings.

We used to, however display settings are generally not saved with the data, so we removed that. Display settings are stored in the mrml scene.
If you want to pursue discussion about this, please start a discourse topic. Otherwise I can implement solution 1 for example.

Do you mean solution 2?

Anyway don't worry, we can manage using Python while we wait for the new OpenGL.

Yes, sorry :)
OK, if you'd like me to do that, please ask. If it's not critical, then I agree that we can wait for OpenGL 2.

Should we only apply the opacity heuristics when importing from DICOM?
Or should we at least make it optional (add a checkbox in the Add data dialog)?

I like the IO plugin option idea, but I'm not sure it's better than adding it to application settings. I think if you have to uncheck it every time you load a segmentation it becomes annoying, in which case app settings would work better.

We could implement both. Configuring through IO plugin properties would be mandatory (so that programmatically you could select the behavior without altering application settings) but default behavior could be stored in application settings.

@pinter Is there a chance it could be fixed in a few weeks (to be included in the upcoming stable release)?

Yes, I'll address this.

Fixed in https://github.com/Slicer/Slicer/commit/82bf550405a5b0dd7f914697c5ce967c6deac8f6