I've got the same problem.
I can see that there's updates on my iPhone, iPod and iPad but when you check in iTunes, it goes off for a quick search ("Accessing iTunes" 2-3 seconds at most), but doesn't display any message at all after that. There should be at least a "No New Updates" message.
I still get podcasts ok and can download the apps again (search for them in iTunes) to get the updates that way, but it's a pain and I've got over 2500 apps now.
I've even tried reinstalling iTunes and everything is up to date software wise, but nothing seems to work.
Cheers,
Mike.