[BrianG]

That makes sense. The on-board BEC also provides power to the control circuits. And BECs need at least 1v higher than their value (need 6v input if they are rated for 5v out). If the battery voltage drops low enough, the BEC is dropping low as well and is most likely rebooting the control circuits. This dip is happening long enough for the controller circuits to reboot, but not long enough where you'd notice any effect servo operation. Since it takes time for the ESC to re-arm, that is noticeable.

Possible solutions:

Running 7 cells should cure this.

Or just run 3s all the time.

Or, if you don't mind a loss in top speed, gear down a bit. This will pull less battery current and will not cause the battery voltage to drop as much.

Or, dialing in a little punch control should work too, but probably won't have as much effect as gearing down. But at least you wouldn't lose top speed this way.