I do encounter a similar problem. I'm quite sure its not hardware related (power supply). I've tried to upgrade
a copter which has many successful flights with a current version (3.5-rc8) of the ardupilot binary.
With the new binary I also see repeated resets. The apm log cyclically shows the following messages
Raspberry Pi 2/3 with BCM2709!
MS5611 found on bus 0 address 0x00
PulsedLightI2C: bad version 0x00 0x00
MPU: temp reset 2395 0
Interrupted: Segmentation fault
This seems to be the same problem and it does not happen with the software originally supplied by Erle Robotics.