Being lightly loaded sounds like the culprit. This is from the MPC data Sheet:
At no load or light load, the converter may operate in pulse skipping mode in order to maintain the output voltage in regulation. Thus there is less time to refresh the BS voltage. In order to have enough gate voltage under such operating conditions, the difference of VIN –VOUT should be greater than 3V. For example, if the VOUT is set to 3.3V, the VIN needs to be higher than 3.3V+3V=6.3V to maintain enough BS voltage at no load or light load. To meet this requirement, EN pin can be used to program the input UVLO voltage to Vout+3V.
Thanks septillion, avr_fred. You were both right, I was testing it on no load. On very light load, it dropped from 3.9v to 3.5v. I appreciate the replies, now I know it requires a minimum load to run properly.