Like other colleagues here, I have tried to reproduce your problem (16 levels at same elevation). No success!.
The problem is serious and deserve attention.
My suggestions:
1. Save the file as a different one name (as a backup) and try again.
Sound illogical but it is a test.
2. Inform us about SH3D version and OS.
3. If you trust us share the file here to study it.
Some of us will find the problem.