it seems to be because your context elements contain transparent alpha values.
the matrix export is doing exactly what you tell it, and exporting with transparency (for formats that support it, such as png), and the image viewing app (Preview on the mac) is matting your transparent image with some solid color, probably grey.
either create a fully opaque black background layer, or don't export a format that supports transparency.
let me know if that doesn't fix the problem.