Sorry for the slow response. Your workaround looks reasonable. Because not all labels are found for all subjects, you might consider using a renumbering script, @SUMA_renumber_FS, instead of 3dRank. Usually that script is now called with @SUMA_Make_Spec_FS. It makes it possible to use the same index across all subjects and to use the various output segmentation masks.

That label for mean_molecular_layer_HP is from FreeSurfer It is listed here as FreeSurfer's index 214. The reranking must be putting that exactly at an integer value, while the others are slightly off. If the ROI value exists, and there is a label for that index exists exactly, then all the labels would appear in the header line, not just that one region. For ROIs, you should use integer values, maybe with :

3dcalc -a mydset -expr a -datum short -nscale -prefix mydset_int

Also it's better to display the datasets automatically with an integer color scale for ROIs

3drefit -cmap INT_CMAP mydset_int

[surfer.nmr.mgh.harvard.edu]