The height settings are in your Genesis Slider settings (you probably have already seen this). Anytime you change the width or height of your images, its always best to run a plugin called “Regenerate Thumbnails” – http://wordpress.org/extend/plugins/regenerate-thumbnails/ We all use this plugin, as it automatically adjusts all of your images to fit within the slider, and other areas of your site that uses thumbnails.
Make sure your Featured Images are set at the right size as well. You can check by clicking the featured image link in your page or post editor.
The logo is in a completely separate section and it shouldn’t affect the slider area. The most it can do is push it down depending on its size, but it won’t affect what goes on inside. The issue is really just the size of the slider images. Once you regenerate your thumbnails from the plugin above then it hopefully will readjust everything automatically. If not then will have to see what else could be holding it up.