I am having the same issue. When I first installed Seriously Simple Podcasting and went to Theme Builder to make templates, the Display Conditions dropdowns DID include the Podcast types. I selected Podcast Archive for my podcast home page, but after making a template and loading the page to view it, the page was based on the default site template. Same thing with my header I had made for podcast pages, and my podcast single page. Then when I went back into Display Conditions to check on it, the podcast types were GONE, and they have been gone ever since.
