If you can duplicate your issue with some simple and small amount of sample data and if you sent me that data I could try to replicate this. Perhaps take a few columns from your source table, change the variable names but otherwise use the same variable attributes and create 3 or 4 records with made up data values. Then set up a job like you current job with an SCD type 2 loader. Once you run the job you could send me both the physical source table and the physical target table and I can try and replicate the issue.
Also can you describe the type of source and target data you are using. Are they both SAS datasets? Are either or both tables another data format?
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