You have discovered what the switch is for.
All different gain stages (EQ, fx, clean gain, etc.) alter the phase of your signal a little or a lot; and some of them flip the phase completely. When that phase-altered signal gets combined with either the original signal, or another version with different phase alterations, this can cause huge dropouts in the lows where the two waves cancel each other out. So if you ever find yourself in a two-channel setup where the lows seem gutted out, flip the switch.