Ok, I just upgraded the firmware to 3.8.2, then checked the variance after rebooting, and with pitot tube covered it was reading 0.0 to 0.2 when powering the pixhawk only by USB. Then I took it out to the field for a test flight, and after powering up with the pitot tube covered, the variance was rapidly fluctuating from 0.0 - 5.5 m/s. I cycled the power a second time, and still the same variance, up to 5.5m/s, so I'm wondering if something else is causing this?
The old sensor was mounted in the same location as the MS5525, its an enclosed side bay, so no exposure to sunlight, only difference in this case is powering a Pixhawk 2.1 via USB or a Mauch Hall Sensor via 6S battery. The old sensor never varied more than 2.0m/s
Because of this, as I did before, I manually adjusted the offset value down until the airspeed varied from 0.0 - 0.2, and then did a quick test flight, and airpseed readings were very good, so I think until we can determine a fix for this, I'll probably be best off disabling the self-calibration, and just use a fixed offset that I know works in the mean time.