Oh, you are using an even older version of dcm2niix :). What is interesting is that in my case dcm2niix creates two files for dMRI_dir98_AP:
Convert 55 DICOM as 009/RS_EH_006_009_dMRI_dir98_AP (140x140x92x55)
Warning: Slice timing appears corrupted (range 0..13955, TR=3600 ms)
Convert 44 DICOM as 009/RS_EH_006_009_dMRI_dir98_APa (140x140x92x44)
Warning: Slice timing appears corrupted (range 0..13955, TR=3600 ms)
While in your case it creates a single output:
Convert 99 DICOM as 009/RS_EH_006_009_dMRI_dir98_AP (140x140x92x99)
It could be that the data transition between your system and my messed something up …