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First of all I would suggest moving to openCV 2.4.5. Lately a lot of bugs concerning the included ffmpeg library and the VideoCapture element were fixed.

However, it could be possible that you will need to specify the encoding to be used by the VideoCapture element. This can be done by using the set functionality and using CV_FOURCC('C','Y','U','V') as parameter for the CV_CAP_PROP_FOURCC setting.