In short terms - problem fixed
In longer terms - how? I really don't have an answer for that.
But I'll tell what I did anyway
I already removed the flyback diode yesterday and there was no improvent on the problem. Today I took the ECU to work and took it apart, checked the MOSFET's and they all seemed OK, atleast checking them with the DVM they all acted as a mosfet should. That didn't satisfy me so I check the hole board under a microscope. I actually found small pieces of metal shavings. One between two legs of the Atmel processor and another also somewhere - don't remember anymore where exactly. My thoughts on the shavings are: because the ECU is a second hand one and originally intended for a BMW then I suspect that the bloke who re-did it for an Audi wasn't very tidy (lack of a better word
) There were quite many small pieces of wire on the board when I looked closer.
But hey, who knows:D Well no-one to blame but atleast the problem seems fixed.