I think I had a similar problem with alpha blending a custom control with a custom TGA. What I finally did was set the backcolor of the control to the same color as the parent. So in my case, I have a window with a button on it.
self.toggleButton:SetBackground("....... point to tga file .... ");
I have to make sure I always set the back color of my control if I change the color of my window.
Have you tried the same?
Edit: Another possible way is: self.toggleButton:SetBackColorBlendMode(Turbine.UI .BlendMode.Undefined);
Edit2: You need to make sure you use self.toggleButton:SetBlendMode(Turbine.UI.BlendMod e.AlphaBlend); at the same time as the above line.