Hi Shva,
Unfortunately I do not have an internal circuit of the MPR121, but giving the reasons you mentioned, it is totally possible that may be a current path from power supply to the pull-up resistors to the internal circuits of MPR121 and finally to GND, this would explain this behavior.
The only thing I can think of by modifying the MPR121 registers to avoid this problem is to test it by setting the MPR121 into Stop Mode (all ELEPROX_EN and ELE_EN bits are zeros) and then set the GPIO bit to zero (I don’t think that this can work, but it may worth to try).
By hardware you can make a test by connecting VDD and VREG together (as appears on Figure 1 on page 3 of the datasheet), this way the internal voltage regulator can be bypassed, and probably reduce the current draw you are seen when GPIO pin is low. If this do not work then yes, unfortunately I think that you would need to do mayor changes in the hardware design.
Have a great day,
Jose Reyes
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