Fail-safe is a feature that goes to pre-sets if signal is lost. In Futaba's there's another step that is a low battery indication, and that is a throttle-down mode.
This is reset in flight by going to idle on transmitter and throttling back to get your bird on the ground safely. It's really a different feature then fail-safe, as fail-safe is for loss of signal, throttle-down is a low power warning.
You still haven't said what brand trans/rec your using, I'm curious. I did read your using JR matchboxes, I would guess your with JR all the way here, but what is it anyways?
I'm not well versed on JR equipment so I really can't offer anything there. However, I've been using Futaba for 20+yrs, and have seen them evolve, and evolved with them. If someone gave me a JR transmitter to set-up, I'd have to learn that system, I can and do offer help readily with Futaba though where I'm able. Always learning though.