I have started this dedicated thread at the suggestion of another contributor.
This issue has was raised on the main 'Arducopter 2.8 / 2.8.1 released' thread and can be viewed here.
http://www.diydrones.com/forum/topics/arducopter-2-8-released?comme...
I'm still puzzled by this twitching, however look at the latest log from today and in a little more detail I can see a very small change in the THR IN trace which appears to be directly connected at the time all the motors twitch (see below).
Is the THR IN trace taken straight from the Rx ?
Not only have I done the things as detailed in the main thread, but I have also:
Grounded the aircraft (in case of interference)
Repositioned Rx to top stack
Reprogrammed all ESC
I have attached the latest log.
Would dropping the ESC Update Speed in MP from 490 - 400hz help ?
Any suggestions would be appriciated, in the mean time i am trying to get hold of a duplicate Rx. Any chance it could be the APM ?
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Until we have the right hadware to know exactly what's going on here, we will eventually send you a debug ArduPPM version so that we can check if the problem do come from the ppm encoder, or from the decoding side in the AVR 2560 chip.
The APM log is not usefull here to give us the exact problem location.
We discussed a lot about this problem in the dev team but unfortunately without deeper testing we are just guessing the root cause.
I'll come back with hopefully better news.
Permalink Reply by Steven Tisseyre on December 7, 2012 at 3:15pm 
No i just saw it. Thanks this is very interesting information.
Permalink Reply by Uwe Blumenhofer on December 8, 2012 at 1:29am
Permalink Reply by Uwe Blumenhofer on December 8, 2012 at 1:37am All Version of PPM Encoder in the zip

Thanks Uwe, but this kind of problem has been reported by me to the dev list for months, well before the release of the older version inside your zip (2.2.64).
Permalink Reply by Steven Tisseyre on December 8, 2012 at 10:25am Thanks Uwe, I'm currently testing version 2.3.13 and initial results look very good.
Its excellent if you have seen no spikes on 2.3.12 also.
Here is a 10 minute bench test flight, nice smooth traces on all channels (just PITCH IN shown below).
Still need to do 10hrs worth of test flight, but looks good so far :-)
Permalink Reply by Uwe Blumenhofer on December 8, 2012 at 3:46pm where can i find the Version 2.3.13 of ArduPPM Encoder

Is only for the tester at the moment, a debug version...

Please PM me so that i can send it to you.
Olivier
Permalink Reply by weelian soh on December 9, 2012 at 10:39am I have similar issues as well where I almost crashed my Hexa after updating to 2.81, so far unplugging and plugging the battery to re-initiate my APM2 seem to make the problem go away for me, I also took time to cable tie down my loose wiring. My spikes behavior looks exactly the same from the videos you posted. I'll be keeping a close eye on this thread.
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