After upgrading to 4.09, the packet I was working on disappeared. When I tried an update from the BOINC gui, this message appeared. My preferences split time between predictor and climateprediction, but since predictor still relies on the 3.xx client, my computer is sitting idle.

What preferences, changes need to be made to start processing again?

This message simply indicates that you have downloaded four WUs (I think) in the day and none of them ran successfully. As your previous WU was running properly under 4.05, I agree that the problem must be related to the upgrade.

Most of us are running 4.09 quite happily, so I suggest trying a full uninstall of BOINC, a reboot, and installing BOINC from scratch. Make sure that you have a copy of your account ID etc first! I doubt that there is anything you have done wrong, and your preferences etc should be fine, but of course you will need to go through them after the re-install.

Best of luck - I hope you find everything is OK, but if not, let us know what error messages you get. These should give some indication of why the WUs fail, even in general terms.