So it actually reads the old statement as

SELECT

 S.IIATransactionId,

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

FROM

 iiafeedtransaction S

LEFT OUTER JOIN

 ratsiiafeedtransaction o

ON

 S.IIATransactionId = substring(rats_filename,   1+patindex('%{________-____-____-____-____________}%', rats_filename), 36)

and

 o.Rats_filename IS  NULL

ORDER BY

 S.IIATransactionId

The explanation is really simple:

With the old syntax it's impossible to determine what part of the where statement is used to join the tables and which part is used to...