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Ingo,
If your using raw processing the extra noise you might be seeing is because of the 14-bit versus 12-bit. In the 40D the signal (and hence noise) will be amplified roughly 4x more than the D50 because of the 14-bit versus 12-bit raws. The thing that is important is Signal to Noise, so more noise is OK as long as you have more signal (i.e sensitivity).
Terry
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