Some folders in the browser view, such as PC presets, Audio loops and few other folders are empty. My install was normal 1 through 4 and then the update X3B update appeared to install ok. I can see the presets and content in these folders in the cakewalk content folder, so why are they not showing up in the browser view?

Did you install content to a custom location? Perhaps the presets weren't updated when you did so.
You should be able to manually navigate to the right folders and resave those presets in the browser by overwriting them.