Hi
This may be unrelated but I’ve just had problems with a magnetometer falling over after a few minutes on a Omnibus F3.
Problem was data corruption on the I2C bus. I solved it by adding two pull-up resistors (1K) at the SCA and SDA connection pads with other ends to the 3.3v supply.
I had to do this inside the GPS puck as the mag. 3.3v supply is derived from a voltage regulator inside the puck which is powered by 5v. It was a bit tight but using surface mount 0805 resistors was good
It works a treat, very stable
HTH
Cheers
Steve 
PS if opening a GPS up, take the opportunity to check and resolder the wire connections. QC on these is notorious 