Adding logo with Alpha channel to Quicktime and exporting as .mp4

I'm adding a PNG file with alpha channel to my existing movie file using "Add to Selection and Scale".
I then have my movie with the overlayed graphic.
When I then Export as an mp4, the alpha channel is ignored!
Any help, anyone?

Yes it looks perfect in Quicktime.
But for some reason I can't save it as anything else or even export a still frame without the alpha being ignored and the image going all fuzzy.

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