Mission Planner saying you have a 3D Fix does not mean you can use GPS modes.
Yes, I know its confusing.
This anomaly was introduced with EKF, which may or may not be happy with the 3D Fix.
Before arming you need to change into your GPS modes and check the LED colour.
If the EKF is not happy then the LED will turn blue again.
If armed check Mission Planner flight mode to be sure it actually changes mode.
I thought the PrecLoiter function was supposed to be in lieu of the GPS. Would it still function if the GPS was jammed or otherwise had a loss of signal while in PrecLoiter?