Hi @Bonita_Mc,
I am assuming that the feature.tax_assignments.txt file is the one from SILVA? If so, when / how was the SILVA reference file made? Or are these taxonomic assignments from Novogene? I ask because when we generate SILVA reference files, we use "doimain" / "d__" and not "kingdom" / "k__".
Also, SILVA is also in the process of updating its taxonomy to be more similar to Greengenes 2 in some cases, e.g. as of SILVA 138.2, they've updated some phylum and genus labels. Perhaps try making your own SILVA reference database as outlined here, and re-classify? Keep in mind, many facilities might curate their own SILVA (or other) database differently and they may not even be equivalent to each other, leading to different assignments. You do not need to follow all the steps, in the tutorial. Much of it is just showing off all the things you can do.