I am building a site as once I have uploaded links work but only when in the lower half of the page. Once they are scrolled to the top they stop working.
Without a link to your live site, I can't say for sure. But if I had to make a wild guess, you probably have overlapping content in your Muse layout. Overlapping content would put links out of reach.
The simplest way to find a fix for your issue: Share you .muse file via Dropbox or a similar service with us so we can have a look. You can reduce your site to one single page demonstrating your issue. This simplifies upload and investigation time.