I have tested the beta 7 of U3 and the general performance drop is still there. 
I get 10 fps less than in beta 5 and olders in the exact same game scenes.
Did you file a bug report with a project that has the performance drop? What’s the case number?
Sorry but my project is pretty big and I can´t send such a file because the size. However I can try to make a stress scene for testing (simulating my scene) and then you can compare the results between beta 5 and beta 6-7.
We found a serious performance difference in calling OnGUI functions (GUIUtility.BeginGUI, all ‘self’ so this isn’t a problem in the our OnGUI code) between Unity 2.6.1 and 3b7. This to a degree that our 2.6.1 game spends 30% of its time just with the invoking of our OnGUI functions in b7. A bug report with example was submitted yesterday.
I don’t know if this is related to your problem, but if you use a lot of OnGUI functions, it might.
Yes, I use a lot of OnGUI functions…