I didn't see anything in the outputs showing :
'Clustered Index Data Row Filtering Predicates' for RSIndex, but this might be because there are no columns being searched in the query that are in the clustered index key.
I don't think this is about duplicates. It seems to me that on one server the data is ordered very differently than the other server, has the clustered index key changed?
Can you get an optdiag and sp_help output for both tables on both servers?
I cannot understand how the new optimizer outputs can be the same if you have rebuilt all the non-clustered indices. At the very least the 'index page cluster ratio' (ok, this isn't used directly in the datapage LIO costing specifically, but still...) has to be approaching 1 for the newly rebuilt indices.