You need a professional WordPress theme developer to fix the problem with the theme. The theme should be looping through something, it's a fundamental feature of WordPress (
read more here). If the theme doesn't do any looping with functions such as have_posts() and the_post() inside of a loop, then WordPress itself will assume that the home page load should load the latest 10 blog posts with the most recent post being the first one in the loop. At that point, calling the filters without modifying the loop in anyway, the plugins will assume that the latest post that WordPress loaded is the content it is modifying. More correctly,your theme should be calling the_content(), rather than calling apply_filters('the_content', $content) with it's own $content.
To explain in logic, when you call the_content filter, PowerPress (and other plugins for that matter) will call loop functions such as get_the_excerpt() or get_the_ID(), which do not correspond with the actual content your theme is loading from some $box1-3. Technically speaking, if the box1-3 data isn't even from a blog post or static page, it shouldn't even be using the_content filter.
A shot in the dark that may fix your problem, though it's still not correct, is to go into WordPress "Settings" > "Reading" page and for the first option labeled "Front page displays", select "A static page", then with the 2 sub options, make sure for the "Front page" you select a static page that does not have a podcast episode in it. You will also need to create another static page with no content in it that you can then select as your posts page with the "Posts page" option. Again, this is a 'hack' to fix a poorly written theme home page, and I'm not exactly sure it will work but it should in theory.