Upadate.
To test the clock speed I tested the board with this code
void setup() {
pinMode(17, OUTPUT);
}
void loop() {
digitalWrite(17, HIGH);
delay(10000);
digitalWrite(17, LOW);
delay(10000); }
And flashed it as 5v/16Mhz Pro Micro. It actually worked with the correct timing. Now I am even more confused. Is this board actually working at 16Mhz with a 3.3Vcc? isn't that adviced agaisnt in the ATmel 32U4 Data sheet?