Sorry, but we need more info.
Output file is SSL doesn't really tell us anything. SSL simply means Single Source Layout. Think of it as a recipe card used to create a specific dish. We need to know what "dish" you are creating. WebHelp? FlashHelp? Compiled CHM? (known as Microsoft HTML Help), MultiScreen? (If MultiScreen, is it just one of the six or so types or is it all?), AIR Help? (If AIR Help, is it browser based or desktop?). As you can see, there are many flavors to choose from.
Are all hyperlinks broken only in a specific browser? You say things are working fine in Firefox, which implies some other browser doesn't seem to work. If so, WHICH browser seems broken?