This might be user error, but I'm seeing some inconsistent behavior.

Everything looks fine in the designer. (Here is testing with fill.)

And it even looks fine in the player preview, but take a look when I launch the player.

Notice in the player, the continent borders, anchors, & stars are all grayed out (These are all areas where the board image should be completely transparent).

It also looks messed up in the Boards->Board Designer preview thumbnail (the entire thumbnail is grayed out), but I didn't get a screen cap of that. 

I get the same behavior in Firefox, Chrome & IE8. 

Do you have a fog layer that has black boarders.

I have no idea if this is the cause, but it might be and would still be a bug as the two above views should be the same.

The only image that is going to show from your Fill image is the areas that are filled by player colors, the rest of the image is not going to show.
So you need to move all your border colors, legend information, stars, etc. to your Board image (but leave the player filled areas on the Fill image).

The way the layers are shown in different places (designer, thumbnail, preview, Flash player) is why you have what appears to be different results.

Thanks Yertle! I think I finally understand how these dual layers work. I had a mental block thinking that the board map was too large (file size) - I had tried compressing it to 8bits, but it always looked like shit, so in my head that meant I should keep the details on the fill map, and just make the board map simple greyscale.

Although I do think selecting 'fill' in the designer, should render the map the same as the player so that you can see what it really looks like without having to start a game.

Sorry to have misunderstood the issue, thanks Yertle.