Comments Plus messing with Headway Leafs

I installed Comments Plus, and it looks great on the post pages. However, it's causing some conflict with leafs.

Here's what my homepage generally looks like:
With Comments Plus enabled:
Site URL: (currently plugin is inactive)

The affected leaf is a html/php leaf containing a java embed code. With the plugin active, it can't be selected/moved/resized in the visual editor. Everything else gets shifted below it.

I'm not sure if the conflict in in the theme files or if it has something to do with the script.