I've searched for similar issues but haven't really been able to find anything even though this seems like a firmware bug.
I've created a waypoint mission like this with a land and takeoff sequence in the middle of the mission:
2. Waypoint 1
3. Waypoint 2
6. Waypoint 3
Once in auto mode everything starts out fine. But when times come for the quad to fly to waypoint 3 (item 6) - the navigation becomes unstable, with the quad doing bigger and bigger circles (extreme toilet bowling). If I flip it back in poshold I can usually bring it to land but it's still affected and want's to fly in circles.
If I don't have a land and takeoff waypoint in the middle of my mission (remove item 4 and 5) - everything is fine, so it seems that something gets screwed up by having a land and takeoff sequence inside the mission.
I'm not sure the arducopter software was intended to have in the middle land and takeoff again, but shouldn't it be possible.
I'm using an APM 2.8 with external GPS and compass and the latest arducopter software, and all other waypoint missions work perfectly.