Update to what is working for me.
Since upgrading to the Beta1, I have tried using the shaper wizard again to get new rules to start with. I made my modifications and had a simpler setup, but the shaper wasn't working as well as it had. As soon as I went back to my previous rules, Beta1 was shaping as well as the previous versions for me.
For those of you who think that the traffic shaping will or should work straight from the Wizard, you will probably be dissapointed. To make it work for your particular situation, it's going to require some knowledge of ports, protocols, packet info and such.
One major bug that was just discovered was the shaper no longer subtracted 20% from the upload and download values. If anyone is having trouble with the shaper please re-run the wizard again and subtract 20% from the upload and download values.