Can you post two straight out of camera shots of the same scene, one with LV and the other using Matrix in VF mode? Be sure to allow the exif data to be intact. Before that, we would be just guessing.
The most common cause for unexpected exposure results when using Matrix is using a FP that is brighter or darker than the rest of the scene. A darker focus point will tend to over expose a little and a brighter then scene will result in under exposure. But in neither case is it s camera "mistake" it is the nature of how metering works and how a photographer uses that to get the camera to capture as he intends the image to look like. Try spot metering and see if the precise spot you metered is well exposed, ignoring the rest of the scene. If it is under exposed, there might be a problem. Stan St Petersburg Russia