APM 2.6 3.1-RC2 Octocopter Alt-Hold motor "pulsing"

I'm having problems with APM 2.6 running 3.1-RC2 on Octocopter. Stabilize works well, but Alt-Hold and any other "automatic mode" like Loiter or RTL is problematic. I've tried default PIDs and played around with them but no luck. The main problem is rather strange motor behavior. 

A picture from datalog is attached, note the throttle on Alt-Hold. I'll also include a photo showing Accel X, Y and Z vibrations, which should be OK.

What could be the problem? Has anyone gotten Alt-Hold to work well on 3.1rc2 Octocopter and is willing to share the values?

altholdthr.png

Accel.png

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