I figured out what the problem was! It is so simple, but it is nothing one think about directly. I know I will in future.
Imagine 2 fans, 1 dm in front of eachother. Each fan is blowing air from the center.. and then 2 Fans in middle and above blowing air out as well from the center. Like below shown.
<-----|case fan|~~~~~|CPU Fan|----->
Now.. between these 4 fans, all air will be blown away. Since the CPU fan need air to cool down the heatsink and the CPU it doesn't get the airflow it needs to do this effectivly.
So what happened was that the cooling wasn't effective. Thus the CPU became warmer and since the fan is thermal controlled there was issued that there was needed more airflow and CPU fan got instructions to work harder. That's why it spinned up after a while and gradually ended up on 5500 rpm and that sure produces a lot of vibrations if there is just the slightest degree wrong towards the center of the earth.
So I disabled the case side fan and put the side back on. CPU Fan now does 3200 rpm and the box is VERY much more silent. As silent it can be with 2 fans blowing air in on front, 2 fans blowing air out on back, 1 fan on top blowing air out (corrected typo error) of the box, 2 fans in the ultra silent power box, 1x3 smaller fans in the lian li hard drives cases, 1 fan on radeon 9800 Pro card and 1 Intel CPU fan
(And imho it is acceptable db, really impressed that it doesn't sound more..).
Being a "Fanboi" isn't always good..
Thanks for your help guys (and girls). I will however look for other cooling CPU fans, just because I like to mech with the tech..