How can I get the Ublox GPS work with ArduCopter2.4.X

I have a ublox GS407 connected to APM2 on a quad-x multicopter. With the on board Mediatek disabled by cutting the TX track on the daughter board. I can made a 3D fix and find the home position with the ublox. After adjusting the loiter gain, I have some position hold ability in the loiter mode, the altitude control behaviour became very strange and the auto mode is not working at all. I searched through out the web that APM2 have auto protocol for the GPS, but it seems there is some major bugs when using with the ublox. Any ideas ?

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