I don't know the details of FSL or mricron's NIfTI-2 support, but it is possible that the issue is with the NIfTI-2 library itself. I ran into problems (link) with producing valid NIfTI-2 files with the library last year, and although that is patched on GitHub I don't think it has propagated to a generally released version yet. If you can, it might be worth dropping in the latest library from GitHub to see if that helps.

Regarding your other question, it is possible to create NIfTI-1 images with the NIfTI-2 library, by setting the nifti_type field to NIFTI_FTYPE_NIFTI1_1 (or NIFTI_FTYPE_NIFTI1_2) before calling nifti_image_write().

I hope that's helpful!