Just to make sure that we have all of the facts. Are you running an external bec, with the internal bec disabled.

BTW, I believe that all the cap in the 3rd channel does is to help to compensate for the voltage drop of the battery, so that the radio doesn't shut down. It really doesn't help much with a lipo pack. It isn't going to stop radio interference.

The only thing that I can figure is that you are pulling much more current when running the lipo pack so there is more interference.

Try moving the radio farther away from the motor and esc.