In my expierience, the first few days of running a closed loop will cause a huge amount of microbubbles. As the plumbing ages, it will go away. See my thread, at first I was plagued with bubbles, but now it is fine.
As far as the cavitation or rattling noise. My Blueline 40 pump does the same thing. If I open it all the way on the return side after the pump, it will make the rattling noise. But, if I throttle the valve back a bit, the noise goes away.