I am not sure you aware but you can't power off an arduino that has any GPIO or analog inputs connected to any source of power because it will "backfeed " through the internal protection diodes.
(each I/O pin has the anode of one diode connected and the cathode of that diode connected to +5V.
each I/O has the CATHODE of ANOTHER diode connected and the ANODE of THAT diode is connected to GND.
If you power off the arduino with voltage on I/O pins it travels to the arduino, through the anode of the first diode and powers the 5V pin (minus 0.7V diode drop) with 4.3V.
If a negative voltage is applied to an I/O pin it is shunted to GND by the second diode.
Atmel recommends not exceeding 1 mA through these diodes but I have powered an UNO (unintentionally of course) , drawing 55 mA this way with no permanent side affects.
If I connect the Arudino's USB to my PC it powers up fine (it runs programs fine and will power the MD25 microcontroller through the Vin pin that connects them). However if I then disconnect the USB power and connect the MD25 to its 12v battery supply, the MD25 powers up (it has LEDs on the board) however absolutely no power reaches the Arduino.
Standard electronic troubleshooting techniques dictate that the connections be checked with an ohmmeter or continuity tester. Obviously there is a problem with your statement that the arduino Vin and the MD25 Vin are connected and the MD25 has power but the arduino doesn't . The arduino Vin is the input for the 5V regulator. If the arduino works with USB connected then it is NOT operating off the onboard 5V regulator. If the USB is disconnected and the arduino Vin (allegedly) has power , but the arduino doesn't , that would prompt one to measure the input and output voltages of the onboard regulator to see if it is damaged. If the symptom persists after replacing the arduino, then one would be inclined to go back and doublecheck that there actually is voltage on the arduino Vin pin.