Hi i'm having problems with my arducopter. It flies perfectly when in stabilise mode. When i flipped the switch into auto mode instead of using the programmed waypoints to navigate to it ends up going in a north easterly direction. In this instance, the opposite direction to the waypoints and continues on this path until it runs out of battery. After recovering it, i tried flying it again today. Perfect on stable mode. when i flipped it into Alt Hold however, it did the same thing and followed the same route until i put it back into stabilise and just landed it. 

I've connected it back into mission planner, loaded the way points and the home location from the board and can see nothing wrong with the points and nothing that would give me a clue as to why it's navigating in the wrong direction. I've also verify the switches on my transmitter match the modes assigned in the mission planner. ie. pos 1 = stabalise etc.

When the apm is connected to my computer it gets a rough gps lock from within my house, so i can only imagine it's got a full correct lock when outside. 

I have a sneaking suspicion that there is a hidden way point hidden in the config, or the home location is set to something other than whats showing in the mission planner. I've downloaded the logs from the unit but can't really make sense of them. 

Has anyone experienced this or could send some light on it. I may try and factory reset the device, but i'd prefer to get understand the problem first so that i can make sure it doesn't happen again.

thanks brian.