And the issue is back! Kind of.Update on this.
It's been over a month and I've had no problems whatsoever. So after all it propably had a bad connection or a strand touching the amplifier's case. I will update if the problem makes a comeback.
It doesn't trigger Audyssey any more, but just randomly goes to protect mode a couple of times a week. It can trigger after two minutes of listening to stereo music or two hours in to a movie. When this happens the power light is blinking rapidly and protection history shows "DC". Low or high volume, cool or warm device, doesn't matter.
Of course I've gone through all the wires, added a fan for cooling etc. It's hard to troubleshoot because the problem comes up so randomly.
Frustrating. The earlier owner only used this amp in a stereo setup and had no problems. And my problems started a few months after purchasing this amp second hand.