Delta Sigma ADC is by principle a Differential ADC. When Single ended mode is selected, the negative input is connected to ground (Vss).
The Delta Sigma ADC's inputs are buffered. If the "Buffer Mode" is chosen to be "Level Shift", then the lower limit of voltage is increased. This might be helpful in your case.
The reason for seeing a wrap around is the offset voltage (which in this case is negative) of the Buffer (or amplifier). Offset correction Registers (OCOR) can be used to correct this. Please refer to the attachment below which explains the accurate ADC measurement an also the use of Offset Correction Registers.