Auto mode wont bypass 20m?

Hi guys build octocopter with navio+ fc, 10000mah 4s battery. I actually had some successful auto mode flight before up to 120m with no problem. I had encountered 2 crashes and got my sd card corrupted and reseted the parameters on my apm. So after recalibrating and everything is working fine except for the compass interference and battery monitor which are also a problem before. EKF compass variance sometimes on flight and hover.

During auto mode with a waypoint at 10m alt the copter flown to it successfully however on the second wp at 20m altitude it moved 1m from wp1 and didnt rise up and just hovered steadily at its initial altitude so I had to RTL it. Tried again with 15m waypoint it worked. Tried first wp at 20m it moved but at an altitude below 10m and its going down luckily the pilot was able to switch back to stabilize before it hit the ground. So we came up with the conclusion that the copter just wont rise up at 20m and has high altitude error is this cause by a bad barometer? or the ekf compass variance error? I remembered the mp displayed barometer calibrated successful before the reset upon connecting to apm but now It didn't do it. Do I need to set some parameter to do this or fix this? 

attach below is my telemetry logs mission at 65.45% I can see error compass variance on my past flight before and it finish the auto mission (set to 10m alt though)

gonna post the dataflash logs tomorrow

2016-03-01-14-31-39.tlog

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