This is a feature, not a defect, as revealed by the message generated:
  Some images have identical time, series, acquisition and image values. DUPLICATES REMOVED.
When you provide the root folder, it identifies that 224 slices of Series 3 (GP_012_20170614125337_s3_0.625mm_Standard) are in one folder and an overlapping 256 are in another. Therefore, it converts all 256 unique images. When provided the child folders separately it dutifully converts all 224 it finds with one folder and all 256 it finds in the other. In your example there are at least partial duplicates of series 2, 3, 601, 602, 999. If you provide a parent folder it is able to resolve duplicates and also combine series that span multiple folders (at least at one time, some scanners only put up to 1000 images in a folder, so series would flow between folders). If you only provide a single child folder, dcm2niix works with what it was given. In general, this method works very well for real DICOM images, but you do need to be careful for software that creates DICOM files with a constant dummy value as the time of day for scanning. It is unfortunate that the DICOM standard does not report how many files compose a single acquisition - that would allow converters to warn you when it only finds some of the images from a series. While we can warn a user if the first image number in a series is not 1, if we see image numbers 1..224, we do not know if this is all of them or if there are missing files.