I assume you are disabling the built-in BEC right (removing the red wire, or unplugging the black jumper)? Depending on which UBEC you are using, it could simply be bad. The DimensionEngineering and KoolFlight UBECs work quite well and have VERy little or no switching noise.
You might want to try adding a small capacitor to the BEC output. That may help eliminate any switching noise. Refer to
this diagram...
You might also want to look at the electronics layout. Keep any low current wires away from the high current wires. Meaning; keep the antenna, servo, and BEC wires away from the main battery and motor wires. High current AC can cause noise to be induced into the other wires.