Is pin 5 the + input that is the input to the effect?
If it is then the reason it is reading 3 volts is because your DMMs impedance is affecting the reading. A lot of DMMs have an impedance of about 1Meg ohm so when you try and measure the voltage at pin 5 the impedance of the DMM forms a voltage divider with the 1M resistor and pulls the voltage down.
Here's a dodgy drawing to make it clearer, because I'm bad at explaining things

Point R 6volts ------1M---------Pin 5
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1M impedance of DMM
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Ground
The voltage on the pin is probably really 6 volts or as you've said the circuit wouldn't work. If you need to measure it accurately you can make a buffer out of a Jfet input opamp connect the probe to the input of that and take the output to your DMM. The buffer will have an impedance of 100s of Megs so it won't load the voltage down.