I think we need a bit more information. 
1. Which QC step rejects all the non-baseline gradients? (look at the report text file) What are the protocol settings for that step?
2. Since you started with a nifti file, you had to first convert it to NRRD? If so, does the header information look correct (the NRRD header is ASCII, so you can look at it with any editor)? Do the gradient directions look correct in the NRRD header?

Martin