I'm having this problem and not finding any hints about it on the web.
After JB (iOs 3.2.1) all my regular apps (more than 100) can NOT be upgraded on the iPad. To upgrade I have to upgrade on Mac in iTunes and sync new versions on iPad. Or delete the app and install from scratch.
If I try to upgrade on iPad error message is "Can't connect to server"
Just to make things more complicated, new apps, just bought on the AppStore, CAN be installed regularly, without any issue!!
Any solutions or ideas?