A) The spacing is wrong in both PDBs. I think this is just an artifact of cutting and pasting into this forum software. PDBs are fixed-column formats, so (for example) all the H’s on the right should line up. (Um, they aren’t all hydrogen, why all H?) It’s possible this is the problem, if it thinks there is a residue named “r”, when clearly they’re rA/rU/etc in your example.
The atom names are totally different. 1H5* becomes H5′ (?) If this is restricted to just the hydrogens, it ought not to cause a problem. If heavyatoms are misnamed, it will cause Rosetta to reject those residues.
C) Which executeable are you using? If it’s not one of the rna_ apps, we might need to hack the database a bit (my coworker did, anyway)…