Well, that seems like a fine form of the command (and it is the most recent form, indeed), nothing jumps out at me as troubling...

Would you mind uploading that dset, and I will take a look?

A couple of side suggestions, and you might already be aware of these, but:
+ there is a much newer version of the NMT available (NMT v2), as described here:
[afni.nimh.nih.gov]
... and described in more detail here:
[www.biorxiv.org]
... where the latter contains direct comparisons showing the improvements in structure/detailing with NMT v2; it also notes that NMT v1.3 (basically, the NMT v1.2 template remade using updated approaches that were developed+applied when making NMT v2) might be a preferable choice to NMT v1.2?

+ The NMT v1.2 and v1.3 only come in 0.250 mm isotropic voxel size. That is tiny! And means that looots of time and memory get used when processing it. There are "lower res" versions of the NMT v2 having 0.5 m isotropic voxels, which are still detailed, but involve less processing (about 8x smaller dsets, memory and spacewise, because voxels are 3D). Basically, for most practical applications, I think the 0.5 mm "low res" versions make a lot of sense to use.

+ The NMT v2 comes with the CHARM (Cortical Hierarchy Atlas for the Rhesus Macaque), also described on an AFNI webpage:
[afni.nimh.nih.gov]
.. and in the above bioRxiv draft. There are 6 levels of the atlas, at increasingly higher spatial resolution. You should read the paper for more details, but it has some practical benefits over the D99 when working at lower resolutions that most practical datasets have, I think.

Sooo, those are a few plugs for altering the base template in your study, which may or may not be practicable at this point. But let me know if you would like me to take a look at the alignment stuff in more detail, with the dataset itself.

--pt