Lars-

I think you will want to check the providence of these images. Possible explanations:
 1. 4D MRI sequence (fMRI/DWI) was interrupted mid-volume, so not all slices are available.
 2. Not all the files were copied to the memory stick.
 3. Data stored in multiple sub-folders (~/dcm/a, ~/dcm/b) and dcm2niix input was subfolder (~/dcm/a) rather than root (~/dcm). This issue would be more common with GE systems that store a maximum of 1000 slices per folder, so a single series can be saved across sub-folders.

In any case, my suggestion of renaming your DICOMs and inspecting each series should be a good starting point. 

Feel free to share a sample dataset directly with me using DropBox, Box or Google Drive. If required, you could anonymize these first (e.g. gdcmanon).