I don't understand how it's a Vref of 4.5v if it's being seen through a 1M resistor, but I'll push the 'I believe' button for now
The input impedance is very high (10^13 ohms according to the spec sheet) so ideally there is almost no current flowing through the 1Meg resistor, thus the voltage at the input of the opamp is 4.5V but in your case it won't because you don't have a blocking capacitor between the pickup output and the opamp input. Without that the pickup's DC resistance functions as a resistor to GND and the opamp input can't be biased to 4.5V.
