You will note that in the Bluesbreaker, the wiper of the Gain pot is tied to the output of that first op-amp. What that means is that when you move the wiper, it simultaneously adjusts both the feedback resistance of the first stage and the input resistance of the second stage.
In the first stage, reducing the feedback resistance decreases gain. because the second stage is an inverting op-amp stage, changes to its input resistance also alter the gain; smaller input resistance = more gain. The way the stock circuit works, moving the wiper clockwise increases the stage-1 feedback resistance and decreases the stage-2 input resistance at the same time, increasing their gains simultaneously.
Now, it also happens that in an inverting op-amp, factoring out all the other factors that can influence it, the input signal to that stage is also a function of the joint action of the input resistor and capacitor. For any given input resistance value, making the cap value smaller raises the point where the low-end is being rolled off, however it does not affect the gain per se. In contrast, making the input resistance value smaller, while holding the cap value constant, results in both the gain changing (increasing), at the same time that the low end rolloff starts to move upward.
So, ignore all the complications and let's assume, hypothetically, that the input to IC1b consisted only of a 4k7 fixed resistor and the .22uf cap. With a 220k feedback resistor, that gives a gain of x46.8 (that may not seem like much, but multiplied by the gain of stage 1 it gets big fast). Where is the low end rolloff? Around 154hz. So, not too much bass cut. Okay, now imagine someone wanted to goose the gain a bit, and decided to do it via reducing the input resistance from 4k7 to, say, 3k9. At the same time, the 220k feedback resistance is held constant. The stage gain goes from just under 47 to just over 56, and the low-end rolloff moves up to 185hz. So, you can see that one starts to lose bottom end as the gain is increased in this manner.
Does that explain what's happening to your pedal?