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Hubert,
Have you tried creating an HTML banner that is just empty. Apparently the logo will not display by default if you choose a HTML banner:
http://resources.arcgis.com/en/help/arcgisonline/index.html#/Using_HTML_to_create_a_home_page_banner...
Here is a good link to show you how: http://blogs.esri.com/esri/arcgis/2012/06/20/create-a-great-organization-home-page/
Regards
Anthony