To get the Execution plans to match between the old and new syntax, the "old style" join query needs to look something like this:

SELECT

S.IIATransactionId

,substring(rats_filename,1+patindex('%{________-____-____-____-____________}%',rats_filename),36) AS OracleTransactionId

FROM iiafeedtransaction S,

ratsiiafeedtransaction o

WHERE...