Understanding the 2N2222 transistor, Where is this voltage coming from
The voltmeter is high-impedance, so the emitter of the transistor is not connected to ground. You should instead connect the emitter to the + terminal of the ammeter that you currently have in series with the voltmeter. That will ensure that the emitter node is shorted to the voltage source negative (ground).
As for why you measure 3.12 volts - in the configuration drawn, all three terminals of the transistor are disconnected when the switches are open. So, the voltage is arbitrary - maybe the simulator solved for that in an initial condition search, or maybe it's a value left on an internal capacitance inside the transistor if you've been toggling the switches while the sim is running.
Note that in the configuration drawn, your base voltage will be much higher than the knee voltage of the base-emitter junction (around 0.65 V at room temperature), so all that'll happen is you'll sink a whole bunch of current from the base to emitter while also saturating the transistor. You probably want to either add a series resistance to limit the base current, feed the base from a current source, or slowly creep the voltage up from zero until you hit the knee (Vbe vs base current is exponential when fed from a voltage source, just like any diode).