In your "Usage" directions you have two screens that I have never seen on any of my wordpress sites. Under "Using the WordPress Media Library" there is a screen with an "Add Audio" musical note icon. That row never appears in my posts or pages on any of my sites and they all have WordPress version 3.5.1. They use different premium themes and a few have Genesis but I'm not sure it's a theme that's suppressing them. Under that image is another one with the "Audio Player" button listed under the Media Title, Caption, Description, and Link URL. I've never seen that button either.
What I've tried:
--at three different sites with different premium themes (one was Genesis, two were not), I've done the following and they still didn't appear in posts or pages
--disabled all plugins
--tried to add media and when buttons didn't appear, disabled audio player plugins
--tried in both posts and pages
--tried in Media Library screen, no button there either
Was that a plugin you used to get that button? Or a configuration for the audio player? I'd like to know. I have all three of these sites on HostGator. I know they sometimes add plugins during installation but I've removed them all because they conflicted with other plugins.