Take a look at the individual scoreterm breakdown. Is there a particular term which is giving you the difference? It may be that the backrub application is adding additional scoreterms like constraints or chainbreak terms, and these may influence what your scores are like. Another possibility is that backrub may be reweighting a term internally. (In the output PDBs it should list what the associated scoring weights are.)
The other (remote) possibility is that the limited precision of the PDB has changed things. When the generating application calcuates things, it uses the full precision of the atom positions. But if you output the structure as PDBs and then rescore them, you’re limited to 0.001 Ang precision. This rounding changes atom locations and thus energies. 30% difference is pretty massive for such a small movement of atoms, though, unless you’re right on the edge of a major clash or something. I mention it as a possibility, but I really doubt that it’s the case.
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