Yokatta! I'm glad that worked for you. That should be one of the first things to check...

In my case it was truly bizarre. My theme layer was selected, but it still wasn't working. In the Advanced tab-->Your Layers, under my theme layer that I made called "additional customizations" there was another layer, a user layer that was called "auto-generated Customizations." I certainly didn't make it, and I couldn't make it go away until I deleted it. When I did that, I lost all my non-code modifications that I had made in the "customs options" tab, although all my coded customizations came back. It was a huge headache.

So my original code was intact and still there, but a new layer had appeared which had hijacked my layout. Does that make sense?