As you suggested, Rosetta isn’t quite happy with the way you’ve formatted the RNA PDB.
For some reason, RNA appears to not be in 3.2, but it was in 3.1 (and I guess 3.0).
Do you have an rna integration test in the folder rosetta_source/test/integration/tests/(rna something?) You can compare that RNA PDB to your own RNA pdb to see what format Rosetta expects. You can also examine the RNA residue types; I don’t know where they are in your copy of the database but it will be something like rosetta_database/chemical/residue_type_sets/(rna?)/types/*.params.