I am sure that I do not like this solution, but it works for the time I have to spend on it.
.navbar .container { height: 2em; }
I also needed to add some padding-top to the same selector to make things inside the navbar align well vertically.
edit: I just re-read your question and see that you have problems with the "divs below". In this case, you also need to adjust the gasket on the body tag, for example
body { padding-top: 6em; }
for Twitter Bootstrap docs on Navbar :
When you attach the navigation bar, do not forget to consider the hidden area below. Add 40px or more apdding to <body>. Be sure to add this after the main Bootstrap CSS and before the extra responsive CSS.
Chris
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