Haven't been able to find anything recent about this. Got my quad flyable yesterday evening. Using default PIDs was able to hover on a tether, then without the tether as everything seemed ok.
APM2.5 /w 2.9.1
850kv 3DR motors
30 amp RCTimer ESCs
Spektrum dx8 with AR8000 DSMX receiver (both the AR8000 and DSMX unit installed)
3DR telemetry, 900Mhz
After flying for a few minutes the motors surged momentarily. Might have been a .25 second blip. Thought that was weird so I switched to the remote config page, and without any throttle changes it was jumping up to 100%, then returning to whatever throttle setting it was at. I figured it was RF interference, so I disconnected the ESCs and watched with the throttle at 0%. With the ESCs disconnected it was still jumping. I disconnected the battery and powered from USB, still had the "jumps." I calibrated radios, reflashed 2.9.1, basically ran through the entire setup procedure.
If it's not interference, and not setup, I don't know where to look aside from another transmitter and receiver which I don't have access to.
I'll be away from my quad for the next week, so looking for any suggestions I can try when I finally get home.
You can also upgrade your PPM encoder to the newest firmware. Once I did this I no longer experienced glitches on any channel at either 22ms or 11ms.
I think this is the right blog: http://diydrones.com/profiles/blogs/new-arduppm-firmware-version-2-....
If the PPM update is too scary just stick to 11ms for now. That worked fine for me for about a month before I updated the PPM encoder.