I think a lot of people have been using “Starter” master pages from different sites and have a similar issue with the functionality of the ribbon.
You’ll notice on an Out of the box v4.master that when you click any of the ribbon buttons to show the ribbon the header and the top navigation disappear. Using the custom master pages this functionality is missing. WHY you ask, Simple there is a div with the id of s4-titlerow that the jquery looks for to hide when the ribbon is visible. With the custom master pages this is missing , removing the functionality. To get it to work just place the class around the header and navigation and you’ll have the functionality back.