From the photos it does seem like everything is mounted ok, the GPS/Compass are on a mast away from interference. The APM is mounted onto a anti vibration plate. My only other suggestion would be to double check your compass calibration, and other settings again. It might be worth loading the firmware onto the APM again and starting from the beginning.
Otherwise can you send me the log files from your flight so I can have a look to see if I can figure out what is causing the problems?