It sounds like you may have a short circuit on the Shield Shield between 5V and 3.3V. USB feeds through a reverse polarity protection diode to VIN on the Electron. VIN on the Electron is connected to 5V of the Shield Shield, and 3.3V on the Electron is connected to 3.3V on the Shield Shield. You can measure between 5V and 3.3V on the Shield Shield with power disconnected and see if there is a direct low resistance. If you do actually have 4.38V on the 3.3V line… the STM32 MCU on the Electron is probably dead. It has an absolute max rating of 3.6V. So if it’s not dead, perhaps there is a measurement error.
FYI: Did you remove U1 and U2 (TXB0108PWR) from your Shield Shield? They appear to be missing. Check for solder shorts between the pins there.