What is the explanation with shorting vcc and gnd to power up the whole circuit in a breadboard?
It sounds like you had a mechanical issue with poor connections, which was temporarily cured by a bit of arc welding.  I doubt anything electronic occurred, you just got some weird lucky break.  Normally shorting Vcc and ground will explode, destruct or evaporate the weakest link in the Vcc and ground wiring between the short and the power supply.  

On an overcurrent-protected power supply, shorting Vcc and ground will cause the power supply to crowbar, i.e. Shut off and re-energize, effectively rebooting the circuit. While also, obviously, draining any capacitance between Vcc and ground.   So it does affect the circuit,