Unfortunately, Excel does not place integer values automatically in the common string table when initially reading the CSV, leading zeros will be lost. 
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Few points:

1. If the...

Since the most expensive statement is select into a temp table, my first question would be what are the configurations of both tempdbs and is there any difference between the...

Please post the DDL (create table) script, sample data as an insert statement and the desired result.
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ORM may be good for things like thrashing out PoCs etc., but after having dealt with several systems that started as "Code First", I've seen enough to convince me that...