Hopefully i can assist here as i have had the same problem where my app would not upgrade after selecting "Upgrade All". I have managed to sort out the problem but there are a few things that you need to be careful off. I will share my experiences and you can take what you need from this.
Apps that save information on the their respective internet servers: (Example: StumbleUpon)
1. This is the easiest to resolve. Go to the particular app that has this problem. Select the app until the delete icon appears on the application. Delete the app. Remember the app that you deleted... 😮
2. Go the app Store and search for the app you deleted.
3. Install the application and it will load again.
4. Application is now ready to use.
Apps that save information on your iPad. (Exampe: TouchDraw) Ouch!! if you have not backed this information up somewhere then you are in a bit of a pickle. I have'nt tried really hard to check if the data is backed up on the PC, but if it is then you should be able to recover the data as well. I have not tried this yet. For ibooks i did not have to do anything here. I got all my books back.
1. Do the same process as above.
With "Brainwaves" i could restore my library.
With "iMuscle" the app Store uses your login and installs the app correctly.
And so on.. I think deal with each app individually and you should be 99% successful.
Hope this helps.. 🙂