@pieper You’re welcome.
Highly likely the problem is in vtkITKArchetypeImageSeriesReader.cxx, i have built Slicer master and have done very quick and dirty port of that file (and .h file) from 4.10.2 (only added things related to new VoxelVectorType). And there is no flip. I shall try to find out what exactly is the issue, but it can take several days, and confirm if it will work.
Here is tiny (20 s) video:
