fable_x:
Oscilloscope shows that Arduino interrupted every 1 millisecond
How to fix?
That's the Arduino Timer0 interrupt handler, which is initialized by the Arduino core library and used for millis() and delay() functions, provided by the Arduino core libraries.
If you want to control the controller by 100% low level routines without any "Arduino magic" being active, you perhaps better do not initialize the Arduino core, do not use setup() and do not use loop(), but instead use a sketch like that with a 'main()' function: