andyford,
If I remember correctly, there was a way to tell the database to not output those two bytes but I can't remember how. I vaguely recall it had something to do with not telling it you were doing CSV but rather text or perhaps it was just changing the extension from .csv to .txt. Unfortunately, the problem was from a customer providing the data and they could never be bothered to do it consistently so I end up writing something that tested the first two bytes and only stripping them if they were ord() > 127.
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