Where is the link missing? In the generated NCX or when you look at the ToC on the device?
If the link is missing from the NCX, then you need to check the options for building the ToC. For a conversion, the ToC isn't usually carried over. It is rebuilt from the book using the options specified. The file for the cover is probably just embedding the cover image and has nothing extra that can be picked up as the ToC entry for the cover page. When I want to do this, I add a hidden heading to the file. This will be something like:
Code:
<h1 class="hidden">Title of the Book</h1>
And in the stylesheet:
Code:
.hidden { display: None }
This gives something for the the ToC builder to find without changing what the cover page looks like.