Throttles up more than should and descend when switching to Auto or during Auto mission

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What steps will reproduce the problem?
1. Switching to Auto from manual/stabilize (Majority of the cases)
2. Halfway during Auto mission..between waypoints (rare)
3. End of Auto mission 

What is the expected output? What do you see instead?

It should maintain the altitude and throttle set by user for the waypoints set. 
Happens mostly between Waypoint 1 and 2 after switching to Auto from stabilize. 
Randomly happens..we can fly for many flights smoothly and it can happen on the 
next day the very minute we switch to Auto. Sometimes when we detect the issue, 
able to switch to stabilize/manual and recover but sometimes no response and 
airplane just plummet to the ground. Tlogs show Output 3 increases by itself 
and Pitch seems to hit a ceiling.

What version of the product are you using? On what operating system?

APM 1, APM 2.5 . Firmware 2.40, Firmware 2.67, Firmware 2.68

Please provide any additional information below.

Setups:

Plane: Skywalker 1880/Bixler/Ritewing Zehyr
APM: APM 1/2.5 with UBlox GPS Lea 6/Mediatek GPS & 3DR 433MHZ Telem Set
Motor: OS Motor OMA3820-1200/Turnigy G10 1200 KV/AXI 2820-10 1200KV
ESC : Tahmazo 60A/Turnigy 60 A /Castle Creations Ice Lite 75A(Red wire is 
disconnected as we use seperate BEC)
Servos: 4 X Emax ES08MA
Tx & RX: Futaba 12FG with 7 chn RX / JR 9303 with AR7000
UBEC: Hobbywing 5a, MAX 7.5A switching at 5V /Castle Creations BEC 10A Switching
Battery: 2 x 14.8v 3300mAH parralled to ESC. BEC to supply 5v to APM . APM 
powered separately

Others: PRISM IR Trigerring device, Airspeed Sensor(disabled after one of the 
crashes as we suspected it may have contributed)

Original issue reported on code.google.com by k.rusyd...@gmail.com on 17 Dec 2012 at 11:15

[GoogleCodeExporter]

Just to be sure, you're not talking about going from alt-hold to manual mode 
and having the throttle stick down below half way?

Original comment by legendlength@gmail.com on 27 Dec 2012 at 2:08

[GoogleCodeExporter]

Hi, definitely not,as this is Ardu plane and it does not have alt hold. It 
happens in auto mode. 

Original comment by k.rusyd...@gmail.com on 28 Dec 2012 at 3:31