Unity performance issue (locked at 3fps)

I have experiences weird bug. I have experienced this bug before but I have recently reinstalled my Windows 8 notebook and it looked like it fixed the issue, but after a while it seems to come back (ehm several hours). The computer can handle the game easily on 60fps but something seems to go wrong and now it stucks on 3fps does not happen on any other HW. Anyone has any idea what can be cause of this? (The GPU is almost unused and it takes about 8% of CPU)
(Renderer is 2ms but main thread is 300-500ms)

Try setting the target FPS, http://docs.unity3d.com/Documentation/ScriptReference/Application-targetFrameRate.html.

void Awake() {
    Application.targetFrameRate = 60;

Can someone explain this to me pleas? I found really interesting fix, thats more likely pointing at the fact, that this is unity bug. The fix is starting the game 2 times. Weird huh? I thought so too, but I have done some testing and in every case when 2 instance are running I get about 30fps, when 1 instance is running I get 3fps doesnt matter if instances are editor/standalone standalone/standalone. Happens every single time!

When I give it second thought, it might seem as some scripts are running in singleplayer that are not running in multiplayer but this issue occurs only on one hardware and it doesnt seem probable to me, because even worse HW could run it better.