Is there any difference between rechargeable pack and regular batteries? Are you using the "3-17-2014" firmware?
I'm on the job, what I might do is send you a few different test firmwares to see if I can make the problem better or worse (I'd take either -- even if I can make it worse at least then it gives me more clues).
[Does it help at all to re-sync the controller with the console? Does it do it when you are plugged into the console with the USB cable? When I was testing a few months back, when I went into the other room, I would get a lot of weirdness. It had to do with proximity of the controller to the console. When I walked back into the room with the console it went back to normal. Wondering if re-syncing would put it on a new channel on 2.4Ghz and cut back on any possible interference issues with other devices.]
Sorry for all the questions, just looking for as much info as possible so I can try to recreate the problem here and get working on it. I'm not exactly sure which side of the ball we should be looking (firmware issue in general, or hardware issue with your controller).
I haven't tried with just regular batteries, but I can test it tomorrow. I am using the 3-17-2014 firmware.
My computer is in another room so I turn the controller off..hold the Xbox button until the option to turn off console or turn off controller comes up. Then select turn off controller.
Then I connect to the USB to mini-USB to the programming port (bottom), then press and hold LB+RB+Power button until lights turn on and flicker. Then I plug in the second USB to mini-USB into the power charging mini USB port (front). Then install the rune pack using the software. Once done, I unplug both USB to mini USB's and go back out to the other room and hold the controllers power button.
It does happen way more often with the Akimbo rune pack and when I have the controller plugged into the charging cable. I can set the controller down and then for example the riot shield (COD Ghosts) will strike with nothing touching any of the buttons. Or if I have the pistols out they will fire a single round.
Let me test this out some more with the different rune packs to see if I see a pattern. Right now I always see it with an Akimbo setup with a riot shield. I usually add an activate on/off tac button (tac button #1).
One thing I wasn't sure about was the "Select Playback Behavior"...in order to get my runes with Akimbo to work I have to set it to: "Loop until release, then play once more". Could this be the issue?