When using the latest Round 32 skin (template53), the HTML files receive additional <div id="top"> element. This element is not generated when using other skins.
Remove the special handing in generating the HTML pages, but add a line to all old planetarion.css files:
Code:
#top { display: none }
If you fear modifying already published templates, re-publish them under new names. Say copy template41 to template61 and adjust the skin-to-template mapping accordingly.
That way content and presentation is separate again.