When a structure is imported through the Structure Loader, Bench concatenates all chains in the PDB file into a single long string of residues. The chains will be in the same order as they appear in the PDB file. This reflects the protocol used by Rosetta.
As a result the numbering of residues in chains beyond the first will not match that from the input PDB file. Each residue number in the second chain will be increased by the number of residues in the first chain. Each residue number in the third chain will be increased by the sum of the numbers of residues in the first two chains. And so on.
We will provide the ability to retain your original numbering in a later update of Bench.