I had very similar symptoms with CrushStation. It turned out to be (partial) phase cancellation in my signal chain. I’m running mono-to-stereo [ /dual mono] on my pedalboard, and the ‘split point’ was my AdrenaLinn III. Evidently, the right output isn’t perfectly in-phase with left/mono out.
When I took it out of the signal path, and let another device (PitchFactor) mix internally, the 12dB boost for CrushStation presets was no longer required. That also solved a longstanding problem that I had with the PitchFactor’s HarPeggiator fuzz effects. I’m not saying that this will mirror your own issue, but it may be a diagnostic worth looking into.