Photoshop :: CS5 - Reexporting Gradient Overlays With Transparency?

I am currently using photoshop CS5,
 
I have a layer that is a vector mask over a solid color. The fill of the layer is black, so when i set it to screen it's transparent. I then have a gradient overlay effect applied to the layer that fades from a solid color to a transparency. There is no blending mode applied to the gradient overlay, so it shows up as normal. It looks exactly how i want it to look!
 
The problem is when i try to flatten this layer, or export this layer as a PNG. The black from the fill shows up where it's supposed to be transparent, even though it's not otherwise visible. If i try to delete the fill all together, and use use a transparent block to overlay my gradient, it won't work, as there is nothing for the gradient to overlay on. If i try to make the gradient using the gradient tool and then using the vector shape layer, it is imprecise, and i know of no way to control how the gradient is applied, other than guessing with the mouse.

I have a bunch of these shapes that need to stack and use the exact same gradient alignment, and i need to be able to export them as png's. If i make them in illustrator and port them over to photoshop, there is still an issue with pixels smearing along the edges of my shapes.
 
Here's an example, the appropriate fading is on the top, but when i flatten or export i get the bottom: