Transparency Problem

[Wit119o]

The graphics in my game are transparent for about 1/2 way through the tile and sprite sets but not transparent through the 2nd 1/2 even though they have the same background color(even changed it to make sure). I know there is a way to make it all be transparent because the graphics i am using are from an old mirage game in which they were transparent throughout.

What i have added are Multiple Tilesheets, where each map tile/layer can choose from any tile; and the Set mask Color from Pixel Tutorial from the forums here.