I ran into this issue with a heavily branded SharePoint site we recently upgraded to SharePoint 2010. I noticed the branding elements were being included in the SharePoint dialog.
This is definitely not what we intended for our SharePoint dialogs. Thankfully, SharePoint makes it easy to strip those elements out by adding the following class to any element you want left out:
<!– use s4-notdlg for any element you do not wish to include –>
<div id=”HeaderContainer” class=”s4-notdlg”>…</div>
Now our dialogs are much cleaner! 
