I have generated a new Github issue to address this. I note that Siemens recommends you export to enhanced DICOM. However, at least with XA11 the diffusion information is still preserved (though in private tags). Can you please test the latest development release (v1.0.20190222) and close the Github issue if it resolves your issue:

$ git clone --branch development https://github.com/rordenlab/dcm2niix.gi...
$ cd dcm2niix/console
$ make
$ ./dcm2niix

You can also compile on Windows, but I usually just go to the Development branch Github page, click the AppVeyor button and get the most recently compiled 'Artifact'

While I do not expect any issues, given the fact you are using a new system with a new feature, I would suggest you carefully validate the b-vectors generated by your sequence. You can download the "dedicated document" from the wiki that describes this.