Nikon .nd2 fixes, part 2

Fixes http://trac.openmicroscopy.org.uk/ome/ticket/11873 (QA 7799) and http://trac.openmicroscopy.org.uk/ome/ticket/11997 (QA 7908 and 9207).

To test, import into OMERO or open in ImageJ all QA files and verify that no error message is present and there are no obvious problems with the images (e.g. channels and timepoints mixed up).  As with the previous .nd2 PR (https://github.com/openmicroscopy/bioformats/pull/1159), files can also be verified against http://www.nikoninstruments.com/Products/Software/NIS-Elements-Viewer/.