I have done occasionally to test how a sketch behaves when it is first uploaded and run (which otherwise can't be tested) The OP shouldn't need to do this, and won't help with the issue i think. The 'All Flash Contents' basically erases the (flash) EEPROM as well as the Wifi settings.
It shouldn't matter at all.
I still suspect that either the Flash size isn't the 4MB specified or somehow one of the boot-mode pins are shorting out. Did you solder the header pins on yourself ?