OK...this looks like it could be something to do when using the Bootstrap setting. It could well be that the menu is being affected, as the menu in Rocket is nothing like the one in Bootstrap. So can you verify you have thie setting enabled?
As for the coloured top border that is all governed by the header table height which is hard coded to be 133px. So If you add...
body { background: none; }
to the Custom CSS box in the Rocket themes custom setting page, and save the setting. The coloured background vanishes and you are still left with the same height of the header area.
If you want to make the header not as deep then you could try changing the height:133px; in this line...found in moodle//theme/rocket/layout/default.php to whatever depth you want,
<table style="width:100%; height:133px; margin: 0px;">
Even so this will probably mess up the whole of the site as the banner also has a say in the ultimate height of the header.
Hope this helps?
Mary