When I'm in low rpm, leave the throttle and then come back to the thorttle I feel a knock from the drivetrain and only after a short moment the power goes to the rear wheel.

It doesn't happen if I come back to the throttle real gently, use the clutch or if the engine is in high RPM.

I did the following in the last several months:
1. Engine mounts tighetened
2. Chain tension adjusted
3. Added a missing shim to the rear arm axle (Helped reducing the problem by a little)
4. Rear wheel bearings were replaced
5. Clutch was adjusted

Any ideas for the cause of it?
I'm thinking somewhere in the gear/clutch area.

My guess is the chain tension might be wrong. You might want to post a picture of your chain.

Sure you aren't just really lugging the motor?

Mine did the same thing before I did the 3x3 and jetted it correctly. Does your bike die when trying to idle in first gear and/or die just as you start to engage the clutch?

I thought mine had a drivetrain issue too and was just living with it until the problem went away as soon as I did the 3x3.

Stop lugging the motor, and make sure your chain is adjusted properly. What you describe is normal for any dirt bike when lugged.