http://arduino.cc/en/uploads/Main/arduino-mega2560_R3-schematic.pdfJust left of the paragraph of text is the auto-selector.Since Vin is causing the USB's 5V to be disconnected, it sounds like MOSFET is okay but the on-board 5V regulator has been damaged. The on-board 5V regulator is shown on the top left of the schematic.
=The LM1117 5.0 regulator is indeed burned out, and I have sourced replacements on Ebay.
Quote from: mrwoll on Sep 23, 2012, 05:17 am=The LM1117 5.0 regulator is indeed burned out, and I have sourced replacements on Ebay.Keep in mind if you remove the regulator now, you can continue to use an external supply by providing a regulated 5V to the 5V pin. (Or use USB.)