Why so much GPU usage for an empty scene ?

Recently i have been experiencing some lag with Unity. I upgraded my Unity to 3.5.6 and everything seems to lag and use a lot of GPU. I have been searching a solution for a while now and can't seems to find an answer mainly because it is not because of the grapics or the script but because of unity itself. When i create en empty unity scene, the best i can get is 4ms with frequent 8ms spikes. In my previous Unity project, a fully completed game created on an older version of unity, i get 1ms with 3ms spikes each 2 seconds. The empty scene lag 4 times more than a full game. The thing is i upgraded Unity to get rid of the small spike lag i was having but now it is a lot worse and i was wondering if somebody knew why and how can i get my EMPTY scene to run smoother. I tried using Unity 4 but nothing changed. Quality settings is set to Fastest and it is a default scene.