i tried multiple times to make my alpha channel black when creating the mask map for a new track, no matter what it shows up white for some reason in the editor and shiny ingame.
(http://i59.tinypic.com/f9jxp5.png)
(http://i59.tinypic.com/6r3t48.png)
(http://i57.tinypic.com/348m43b.jpg)
On the Top menu, go to Window > Channels.
You maybe need to add an extra channel here for the alpha to be editable.
EDIT: Ok, I didn't look at your pictures properly. :) You already have an alpha channel in there.
I know you've solved this now by going to Image > Mode, and setting it to 8bits per channel.... but for anyone else reading this... Having 16 bits per channel may cause you issues.