I am using the same design for the two system described here. The first system charges from the USB and runs on a battery. The second system has no battery and runs from a 5VDC supply connected to Vin.
The battery system runs OK but the other system has the intermittent drop out of Vsys. The system with the problem can run anywhere from 20 minutes to 2 weeks before the Vsys drops out. The Vsys goes from 3.6V to zero volts when it drops out. I have measured the temperature of the chip and it never goes higher than 28 degrees C.
I am showing the schematic of the circuit below. Do you have any suggestions on what might be the cause of the problem?