The power supply sounds ok. It’s not obvious to me what’s causing the problem. Two things I would suggestion: 1) take high resolution pictures of your board (under good daylight) of both the front and back of your PCB so I can check if there is any soldering issue; 2) when the problem happens, measure the voltage between VIN-GND and also VCC-GND and see if they are still approximately 5V and 3.3V.