Hi freewill,
Could you post a schematic and I can review to see if I can notice anything that could be causing the issue?
It is very unusual to have current flowing to the negative power supply as all the digital pins operate from the Vdd supply. The only way for current to flow to the negative supply is for the ESD diode to be reverse biased, which would occur when the voltage on the source exceeds the voltage on the Vss pin. Is the supply on the source referenced to the same ground as the Vss supply?
Regards,
Joe