In Remote Apps, I've found a way to add a new section to the secondary menu of the JIRA header that breaks the create issue and quick search bar. Here is the plugin config that breaks it:

<web-item key="general-dropdown-item" section="system.top.navigation.bar" weight="100">
        <label>Remote Apps</label>
        <link linkId="general_dropdown_linkId"/>
    </web-item>

    <web-section key="remoteapps.general" location="general_dropdown_linkId">
    </web-section>

It adds a drop down with no items, that somehow adds a closing div w/o the opening div, breaking the markup and making the quick nav appear on the next line. As Sean for more info.