The issue is with the z-index. This controls the placement of elements over each other (for example text or an image would be placed on top of the background).
Your logo has a z-index of 4, the nav menu has a z-index of 6. As the logo impedes on the navigation area, the z-index of the menu places it on top of the logo, hence the link not working.
To fix this, you need to adjust the size or positioning of the logo (or both) and keep the elements clear of each other. You also need to add this to the end of style.css so the logo link covers all of the logo image:
#top .logo a { width:auto; }