Gaussian surfaces may be slow to recompute sometimes (e.g. for large molecules), so there is an "Update" button to recompute the surface. You need to use it when you change the color.
About the transparency: it depends on the order of visual models. Since order-independent transparency is not yet implemented, you will see the secondary structure only if it comes before the gaussian surface (when you traverse the document in depth-first order).
Here is an example with the Gaussian surface first:
And here is an example with the Gaussian surface after the secondary structure: