Try changing the settings in the [Custom Autopilot] section.

Use whichever of these is the different on to what have in your aircraft.cfg.

[Custom Autopilot]
AP_Roll_speed=3.91
AP_Roll_window=5.7
AP_Roll_controlstep=2825


[Custom Autopilot]
AP_Roll_speed=4
AP_Roll_window=7
AP_Roll_controlstep=1500

The first one is the default v1.1 setting, on which mine flies great. The second is, I think the settings that Captain Sim posted a while back in regards to roll left and right. It was mostly happening during an ILS approach, but it might fix the in-flight rolling problem.