The magjack will be damaged if it gets 12V on some of its pins. The problem with silicone components is that when damaged, sometimes they open up and sometimes they short out. If the magjack shorted out, it may be what is putting such a huge load on the 3.3V regulator and since the 3.3 is fed from the 5V regulator, it will put a high demand on it as well. The condition that you are seeing appears to be what is called thermal runaway but I'm not sure what is changing. It could be that the overheating regulators are beginning to allow more voltage which allows more current which gets them hotter, causing them to allow more voltage and on and on it goes. I would remove the magjack and power up the board and see if the 3.3 still overheats. If not, then you know what needs to be replaced and hopefully, the excessive voltage from the overloaded 3-3V regulator didn't damage the PIC's. Remember that the green LED is not a power LED, it is an indicator that the EDT is operating properly. If the magjack has failed or is removed, it will not light so don't worry about that one until the magjack has either been replaced or proved to be ok.