kinda funny and kinda embarrassing...
the problem was not in the power supply after all.
The power board does a little buzz normally when its not connected and when its short-circuited this buzz becomes high pitched and louder.
so my friend and I concluded that it should be something on the main board
and it was...
I don't remember the part number of this component right now, but it is an electrolytic capacitor very close to the RAM ICs, and the value is 100uF X 6,3V.
It was completely smashed (I don't really know why, maybe I did it myself and didn't notice).
So we just had to replace it.
Anyway, this wasn't a total waste of time (and energy), we understand now how the 3DO power supply works, and will post it here some day soon, so maybe we can help someone that actually has a problem there...
What matters now is that I'm happy I can play Road Rash and Gex again =D
Thank you again for the support