Hi Rui,
I’m on a similar path to you, researching arduplane for my first ardupilot build & I will be using an Omnibus Pro clone too.
So this comes from someone with the least amount of experience you could find … 
Firstly at least with the Omnibus clones (not sure about the original) the main controller is extremely sensitive to voltage levels, so it is wise to power servos from an external source (BEC / PDB) rather than from the board itself - in case a high servo load causes the processor to brownout. Not sure if this is contributing to your issues.
Also elsewhere on this site ( AutoTune woes. what am i missing?) there has been discussion that autotune on ardupilot was not saving parameters in versions 4.0.0 and 4.0.1 but should have been OK by 4.0.2 … so not sure if they didn’t hit target or if something has reverted with 4.0.3.
In any case it may be worth trying to save settings as Dave Glover said in above link by,
Performing auto tune. Land and disarm. Read the settings in mission planner then click write Params.
Good luck