If the datasources of the Merge Join block in SSIS aren’t sorted the merge will not work correctly.

Merge Join

Strange behavior will occur if the datasources aren’t sorted equal by the same key.

http://msdn.microsoft.com/en-us/library/ms141775.aspx

“The Merge Join Transformation requires sorted data for its inputs.”

http://msdn.microsoft.com/en-us/library/ms137653.aspx

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