I just experienced the exact same thing.
After updating iTunes, I opened it and played around.
I then came to the Apps section, and checked to see if any updates were available. There were three, and I clicked the "Download All Free Updates". But it acted just like you describe. I had to click on "Get Update" on each app.
Furthermore I'm pretty convinced that in the previous version, when browsing around in the iTunes app store, I could use gestures to navigate back to previous pages.
This I cannot do anymore. And when I click on the back arrow, it doesn't take me back to the previous page, but all the way back to "My Apps Update" page where it tells me that there are no updates available.
It seems they have released this version of iTunes a bit too early.