While your report is good and descriptive, I don't see anything wrong with what you were reporting.
Let me give you an analogy... Let's say you took your baby brother's toy car away from him, right in front of him. Instead of asking you for the toy car, your baby brother went to his sister to ask for the toy car. While his action might seemed logical to some, it doesn't seem logical to me.
In our case, if you want to let Element Hider Helper manage and elements, simply go inside Flash Control configuration panel (accessible via the sidebar) and uncheck "Block Adobe Flash" (for embed elements), and/or "Block HTML5 Video" (for video, audio elements) I will be adding in yet another checkbox for "Block HTML5 Audio" in the future, but that's another story.
Alternatively, you could just set Element Hider Helper to "not hide" embed, video, and audio elements, if that is available.
Something's got to give, right?