There is input voltage monitoring, and an overvoltage shutdown if the input voltage goes over spec. It could be possible that if your supply is idling quite high and there is some voltage sensing circuitry on the supply that isn't connected, you could have enough overshoot to trip that protection. It would be hard to see with a multimeter, but you could be going over 13.2V.
Try connecting the voltage sense lines as klondike_bar suggested to get the voltage back to 12V, and see if that fixes the issue.
This sounds like the most likely candidate to me. In my testing these supplies operate at the high end of the ATX accepted range though still within it. What is the exact voltage cut off for the habanero to shut itself down if it is less than the accepted range it could be causing the shut down.
The current sense wire that people are talking about is already connected on these boards. What is the voltage range that the Habanero accepts is there any way to adjust that to see if that is the issue?
ATX spec is +/-5%, up to a maximum of 10% at peak loading. The VRM will shut down after I believe 5ms above 13.2V.