LibreOffice, for instance, has a policy that says You can use their trademark if you are 'substantially unmodified', which means "built from the source code provided by TDF, possibly with minor modifications including but not limited to: the enabling or disabling of certain features by default, translations into other languages, changes required for compatibility with a particular operating system distribution, the inclusion of bug-fix patches, or the bundling of additional fonts, templates, artwork and extensions)."
Mike Connor from Mozilla has said that to use the Mozilla trademarks, you have to get prior approval from them for your build configuration and every patch you introduce.
http://bugs.debian.org/cgi-bin/bugreport.cgi?msg=74;bug=3546...
In this case there is more than a little politics involved.