I tried also and got the same results. I think you have found a bug 
in -flatten that should be reported to
http://www.imagemagick.org/discourse-server/viewforum.php?f=3&sid=ea904cad65c4f22e12644da295703031

The following works:

convert in.png \( +clone +matte -threshold -1 \) +swap -composite in_tmp.png

Note:  \( +clone +matte -threshold -1 \) creates a white background image


>Am i doing something wrong?
>
>1. if i run this command on an image with a transparent layer:
>
>>  convert in.png -background white -flatten out1.jpg
>
>... i get an all-white image (This used to work on version 6.2.8)
>
>2. if i run this command
>
>>  convert in.png -background white out1.jpg
>
>... the transparent areas are not-nicely filled with black
>
>3. input & output images:
>
>http://www.mklogo.com/in.png
>http://www.mklogo.com/out1.jpg
>http://www.mklogo.com/out2.jpg
>
>(i tried moving the -background command around ... )
>
>4. I'm running ImageMagick 6.4.1 05/01/08 Q16 ....
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