Several users with futaba radios have reported glitches when using futaba high-speed external receivers and the bank/gain channel. We've confirmed this bug, and narrowed down when it happens and how to avoid it.
The interference occurs between the aileron channel and the bank/gain channel (plugged into the EXT-LED port). For now the work-around is to first set your radio ATV's (endpoints) to their maximum value, so the gain inputs read 100% on the GUI. Then select "lock gains" on both cyclic and both tail banks, and use locked gain values. This will avoid the problem and still allow you to bank-switch.
We apologize for this problem. However we already have it solved here, and that fix will be released in our September firmware update, which will also include s-bus compatibility.