The lower the supply voltage on a BBD, the lower the headroom.
So the BBD in the V6 circuit (that has BBD supply of 9V) will have less headroom than the BBD in the V5 circuit (which has BBD supply of around 12V-13V).
If you look at the 9V circuit schematic you see a pair of 130k resistors at the input op-amp.
http://www.metzgerralf.de/elekt/stomp/mistress/images/1981-electric-mistress-v6-schematic.gifThat means the input signal voltage is scaled by 130/260 = 50% at the input, and that is because the BBD has reduced headroom in that circuit. So signal is scaled down deliberately in the V6 to keep it within the headroom of the BBD.
In the V5 schematic, the resistors near the input opamp are 5k6 and 100k, so the signal voltage is scaled by only 100/105.6 = 95% at the input. So we are not losing half the signal as in the V6 circuit.
http://www.metzgerralf.de/elekt/stomp/mistress/images/1980-electric-mistress-v5-schematic.gifThis explains why the V6 lets through less signal than the V5. There are other changes in capacitor values elsewhere that means the V6 will let through more bass and low-mids, and that partly compensates for the signal loss.
Your problem is most probably down to the BBD bias not being set correctly. You can adjust it by ear.
1) Put in filter matrix mode.
2) Put color pot at minimum
3) Put range pot at maximum
4) Adjust bias trimpot. It should only need **small** fraction of a turn. If bias is set too low or too high, you will first get clipping (signal is hitting either top or bottom headroom limit), and then nothing at all through the BBD. The BBD only lets signals through for a small range of input voltages, and you are trying to set the bias voltage near the middle of that range.
Before doing any of this, you should measure the supply voltage of the circuit first to confirm it is at 9V. If you are running from a battery or a supply that is giving less than 9V to the circuit, then the BBD bias may not be correct (remember correct bias depends on supply voltage) but does not necessarily scale with it. For example, bias required for 9V BBD supply is not necessarily 3/4 of the bias requried for a 12V BBD supply.