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As mentioned in discussion under my other answer, the problems most likely arose from either a bug or corruption in the OpenCV-library I used (v2.3.1-11, prebuilt from 64bit Debian Wheezy repositories).
Building latest version from source fixed my issues, although the method for mask/threshold described in my other answer seems easier and more semantic code wise.
ThresholdedImage=(Original<ThresholdsMAX & Original>ThresholdsMIN) * Original