Lets start with the non inverting input. There is a 60mV drop across the 47K, so that means in input bias current to the opamp of .06/47000 = 1.3uA. Now it should be less then 0.1uA, so something is wrong here. I think the Circuit Wizard is way out of spec for the input bias current for the LM358.
Anyway, lets accept that the drop is 0.06mV. you have to compare all the voltages in the circuit to the DC reference voltage (1.21V), so that makes the input about -0.06V. The first stage has a gain of about 6, so you expect an output of -0.36V which is about right. The second stage has a gain of 6, so the second stage should have an output of -2.16V which it cannot do, so instead you have a saturated low output. So after the input, the rest of the circuit is behaving about right.
Now for a guitar amplifier, you really do not want the same gain for DC as for AC. A 1Hz wave going through to the speakers will not give any useful sound output from the speakers, but it can certainly do a brilliant job in burning out the speakers.
If you add a capacitor in series with the 2K resistors, the DC gain will reduce to unity, so even if there is this odd -0.06V on the input, it will just give -0.06V on the output, while you will still get a total of x36 AC gain for the audio.
Next thing I do not like is that the LED is not a great way to regulate the 1.21V reference level. The current drain from the second stage 2K resistor will modulate the 1.21V across the diode and this will feed back into the first stage causing distortion, given the non-linear nature of the LED. An electrolytic cap across the LED will greatly improve the circuit performance.
In conclusion, the only mystery in the circuit is "why you are getting the massive 0.06V drop across the 47K resistor to the first opamp input". I would expect the output offset on the breadboard to be a lot less than 300mV from 1.21V, but the exact amount depends on the values of input bias current and offset voltage for your opamp.
Richard.