I'm having the same problem with an iPad 3 & iPhone 5. I'm using a PC but my wife also has an iPhone 5 and I upgrade it with a MAC Book Air. She too has updates on the App Store but when you go into iTunes, it says all apps are up to date......
Very discouraging to say the least.
Our's too, started within the last 2 weeks or so. I generally let a few build up before setting up the computer. I use the PC & Mac since I have more than 1 idevice for each of us. Her iPad 1 hasn't updated IOS in a LOOONG time either but it generally keeps up with App updates. Then I plug in the other device and only have to wait 1 time for each of us...