Loop Time

Guys
Anyone know what this means in the log and what I need to do to stop it.
I assume its a problem

07/02/2016 13:00:21 - 004050: APM Speed Error: The number of long running main loops is 438 @ 11.385ms
07/02/2016 13:00:21 - 004050: APM Speed Error: A one off here could be ignored but if repeated in this log,
07/02/2016 13:00:21 - 004050: APM Speed Error: then try disabling some logs, for example INAV, MOTORS and IMU.
07/02/2016 13:00:21 - 004050: APM Speed Error: The total number of sustained loops 4000
07/02/2016 13:00:21 - 004050: APM Speed Error: This is above 5% of the total loops!
07/02/2016 13:00:21 - 004050: APM Speed Error: Try disabling some logs, for example INAV, MOTORS and IMU.
07/02/2016 13:00:21 - 004050: APM Speed Error: Otherwise seek further advice before flying!

Well things are getting more interesting.
I reflashed the pixhawk and now get a compass variance issue.
So for giggle I unplugged the external GPS and did a factory reset on the config of the firmware. Then did a compass calibration. Much to my surprise it calibrated compass1 and compass2, gave me offsets for both and I happily watched the little coloured dots move around with the machines change in orientation during live calibration. Interesting considering Pixhawk only has 1 on board compass and the GPS based compass is not plugged in. My guess and I will confirm this tonight that the internal compass id has been somehow captured as the internal and external compass and this is causing the grief I am experiencing.

IF I can I will reflash it tonight with a back leveled version of the code to see if it clears the issue. Perhaps install plane first then copter just to be extra special safe.

also mission planner gives me a “Ground Start” message which I have never seen before and can’t find any documentation on. Very odd indeed.