I’ve downloaded the data and checked where Slicer gets the exported labelmap geometry and I’ve found that the DICOM data sets are not created correctly. RT structure sets must reference image frames that they are created from. The STS_001 validation data set’s structure set contains invalid references:
Referenced series instance UID in RT structure set:
[0020,000e] SeriesInstanceUID 1.3.6.1.4.1.14519.5.2.1.5168.1900.293609116849698550139986038601 UI 64
Series instance UID of the CT image:
[0020,000e] SeriesInstanceUID 1.3.6.1.4.1.14519.5.2.1.5168.1900.449841255123215696894565592289 UI 64
ReferencedSOPInstanceUIDs listed in the RT structure set file do not match any of the UIDs in the CT image either.
Please report this error to the maintainers of this data set.
Consequence of these invalid references that the RT structure set does not get associated with the CT automatically (Slicer can work with many CTs and structure sets simultaneously, so the fact that you only loaded a single CT so far does not make Slicer assume that it should be used as reference geometry).
You can set the CT as the reference geometry for the structure set in Segmentations module:
Note that the binary labelmap representation that Slicer created without this association were completely valid, too. If they loaded incorrectly in some other software then report this error to their developers. It is OK if a software cannot handle segmentations and and CT images with different geometries (use different origin, spacing, axis direction, or extent), but then the software should detect this and display an error instead of showing incorrect result.