Hi Martin,
I did receive your zipped theme. It took me a while to unzip it, because each single file was itself zipped... Then it took me a while again to find out which files were actually used by your theme, since there were a lot of *.css files left over in the theme directory...
Anyway, I found out that the real problem comes from your header.html file, which you have playing around a lot with, and the result is that the output of a course home page in Moodle is not what it should be: there is no #course-view in it, so of course all the settings I gave in my previous posts could not work on a non-existing division...
See attached screen capture.
I agree with Urs that the best way to understand how Moodle CSS works is to use a tool such as Firefox Web developer, and activate the View Style Information mode. That's how I got the CSS info. displayed on my screen capture, and how I discovered your missing #course-view class...
I have not used greasemonkey, and I see from another post of yours that you could not get it to work and then could not get webdeveloper to work. You should probably completely uninstall and re-install Firefox plus its webdeveloper to make it work.
To come back to your problem, you should start with a clean header.html file and proceed gradually to customize it, checking the results in your Moodle site each time you change something.
I hope this will help,
Joseph