Thanks for the answers guys,
So, the ground from the board, the source pin on the mosfet and the fan are going to the ATX ground. All the others are going to a GND pin on the board.
So how/where did you connect heater supply and heater ground (source of fet).
The heater supply comes from a 12V source on the ATX.
It might be better to power the Arduino with 5volt directly (hacked USB lead).
I thought it was kind of mandatory to power the Arduino with more than 5V? Should I put the 5V wire from the ATX directly on the VIN pin then (if there is no drop)?
I'd look at common earth problems, as Leo suggests. Run the source of the MOSFET and the gnd of the uno independently to the 0v of the 12v supply.
I'll try that. You mean I should use a completely unrelated ground, right?