- Open up iTunes and take a screen shot of all your applications. You could write them down instead, but I found the screen shot a lot easier.
- Delete all the 3rd party applications on your iPhone
- Delete all the 3rd party applications in iTunes
- Exit iTunes
- Empty your Trash. Do a soft reset of your iPhone. (Just for good measure)
- Restart iTunes
- Download all your applications
- Resync your iPhone
I know its a bit of a pain, but it worked for me. Apparently the 3.0.1 update somehow mangled the application files.
Hopefully this post will help the next poor soul that has this problem.