If it worked OK 40 times on the bench since you had the issue, then I would say it is working. Maybe they brakes have the metal disks and there was some lube or preservative on there that got burned off after braking a couple times. ??
Before changing the Rxer, I would test its output with a PWM Meter a couple dozen times. I don't know anyone who uses that brand RF system on Jets, and I have never seen one of those show up at my jet events. So, I can't tell you why you would need more than 100% travel on the Txer. I do have a couple glider pilots who use that brand and have been flying very high with that brand TXer .Those pilots seem to like some of the apparently unique features. But with your LGC's Brake limits set at 100%, you should see some braking when the TXer outputs 100%.
Bumping up the anti-lock ratio increase the frequency of anti-locking cycle (i.e. works the cycle more frequently)
The other circuit to check would be the battery power to the LGC. But those brakes should work with even 6 volts let alone 2S LiPo. If the gear is deploying and retracting consistently, then you have adequate power to the LGC for braking.
I always seem to have a spare LGC15 around getting ready for the next build, etc. If I had this issue, at this point I would swap the LGC out and try the spare. If I had to, I could always jerk an LGC from one of the other planes for testing too. After fiddling around for a couple hours, I ended up swapping a previously crashed one out. You may want to look into swapping yours out or contacting Gaspar directly. It is hard troubleshooting w/o it being on the bench in front of me and working the problem from start to finish. I have given you all the related info I can think of. Please do let us know what you eventually find out. Good Luck!