The problem is exactly same with the topic. I have custom board for Beacon. At the beginning I soldered 5 boards and all of them was working perfectly. After few days, 4 of them started not to work. I tried to reprogram all and all 4 circuits worked. After that point another problem occurred.
When I powered-down the circuit and powered-up again, program didnt start. I discovered that if i reset the MCU with command line (nrfjprog -f NRF52 --reset) MCU is booting up and starting to advertise. Actually it is not relevent with the reset. I just have to wake up the MCU. For example if I make a "verify" or "read" with nRFgo Studio it also works.
What could be the problem?
By the way I setup 2 more circuit and there is no problem something like that.
The code is almost same with the "eddystone beacon" example. I only added 2 timers for starting and stopping the advertisement. Thats all.