tsql not firing (stored procedure via ssis) - SQL Server 2012

I've created one of many stored procedures as part of an ETL process and one of the queries within a stored procedure isn't executing.

The environment is SQL Server 2012 SP2.

The bizarre thing is this -

Run the select part of the insert (affected query) - returns rows

Run the insert (affected query) - inserts rows

Run the whole stored procedure via SSMS - inserts rows

Run via SSIS - all other queries run barring the one of concern!

There are no conditions in my stored procedure e.g. if x = True the Return and no debug code is in there either e.g. return. There are also no transactions and the table I am reading from is a staging table populated prveiously by a data flow.

The query:

INSERT INTO Person.CustomerLinks 
            (PersonID, SystemID, CustomerID_bin, CustomerActive)
SELECT      i.PersonID
,           s.SystemDefID
,           i.CustomerID_bin
,           0
FROM        Staging.IdentifyOutput  i
JOIN        Config.SystemDef        s   ON  s.OutputType        = i.OutputType
WHERE       i.CustomerID_bin    IS NOT NULL
AND         i.OutputType        IN ('L', 'X')
AND         i.PersonID          > 0
AND         i.FileDuplicate     = 1
AND         i.PreferredRecord   = 1
AND         NOT EXISTS (    SELECT  1 
                            FROM    Person.CustomerLinks cl 
                            WHERE   cl.PersonID         = i.PersonID
                            AND     cl.CustomerID_bin   = i.CustomerID_bin)

The procedure has a Try Catch block and the Catch will raise an error and no error is raised.

The only other non ETL code in the procedure is -

SET NOCOUNT ON
SET TRANSACTION ISOLATION LEVEL READ UNCOMMITTED

But I put this in all of my procedures in this application as I am not concerned about dirty reads as they won't happen.

I placed tsql directly after the insert to write to my audit system and @@RowCount was 0. Yet if I run the select now I get over 1.5 million rows back.

Any suggestions?