From the outside the city of Whiterun appears to be invisible except for its wall. If I stand in a high place and look at it I see a large circular wall but nothing inside it. At night I can see all the lights on Dragonsreach but everything else is invisible. It's a fresh install of Skyrim, I've updated my graphics card drivers to the latest ones and the only mods I have are Immersive Weapons, Immersive Armours, Quality World Map and SkyUI. Disabling them doesn't fix the problem. Not sure if other major cities are invisible as I've only got as far as Whiterun.

Any ideas?

That's as designed. Each major city is in its own worldspace and the interior is not loaded until you enter the worldspace. However, if you want to de-worldspace the cities, you can use Open Cities Skyrim: http://www.gamesas.com/topic/1424627-relzwipz-open-cities-skyrim-thread-5/

Cells sometimes don't render correctly. Fast traveling somewhere, then coming back usually fixes it. Although, sometimes a system restart is needed to clear the cell cache. This has happened in every TES game (and FO3/New Vegas). It's not a big deal, just weird when it happens.