The problem with the custom windows were the glass was a tad thick (around an inch to an inch and a half) and the render material was set to "Clear Glass" and not "Clear Glazing". This is all very application specific, but it is definitely something that you want to keep in mind when creating glazing and rendering in Revit. Enjoy and I hope it helps!
- Rendering Materials: Glass and Glazing
- Rendering Comparison of Curtain Walls
- Rendering Comparison of Cubes