Unfortunately, I cannot reproduce this problem. Here is my page with custom CSS and custom theme, working in juxtaposition to what I’m seeing in your page. I have no scrolling issues and I can’t find a way to break it.
It seems like the ‘non-skuid’ elements are not meshing with the skuid or salesforce elements on your page somewhere. I cannot find a more specific answer for you at this time.
If you can create a simpler page outside the customization where the scrolling issue persists, I’d love to take a look at it.
