Not looking for advice, just passing along what happened to mine. I crashed my drone, but the pixhawk sustained no damage. After fixing the damage to the frame, I turned it back on only to get a low-voltage alarm. I even connected Mission Planner, and the software claimed the battery was near death but the amperage was way too high. I confirmed the battery was fine with a voltage/amp tester. Next, I went through all of the connections with a multimeter and found nothing. Finally, I went to a friend's house who had the same drone AND a pixhawk. One by one, I pulled parts of his and tried them on mine until I got to the pixhawk. Once I swapped out the device, the drone worked again without issue. I opened up the device and scanned the board for shorts. There were none, and no singe marks. However, the processor got really hot after being on for only 5 minutes. I still have no idea what happened, but it has to do something with the pixhawk. I'm going to buy another one ASAP.
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Maybe same issue:
http://www.diydrones.com/forum/topics/pixhawk-meltdown-please-take-...
Voltage level translator shorted or desoldered.
Thank you for the tip! After reading this, I checked my translator but found nothing wrong. It was still soldered to the board and couldn't be pried off.