Great news @AndyW!
If anyone who is experiencing lock-ups with CFOD has an easy way to monitor uptime of some polled sensor data, I would be interested to see if my proposal for watchdog timer fixes helps you:
Note this code is basically the latest Core-Firmware Master with my changes, so any other CFOD fixes are not present. I think it's a fair test, and any additional CFOD fixes should make things more stable. The watchdog stuff just keeps the random weird bugs from completely crippling your application.