LTC2496: Regarding calculation

Hi

We are using LTC2496 ADC which is connected to our microcontroller F280025PTSR through SPI. In LTC2496 CH0&1, CH2&3, CH4&5, CH6&7 and CH8&9 are configured as differential channel as follows.

 Channels        address

  8,9                   0xA0
  6,7                   0xA1
  4,5                   0xA2
  2,3                   0xA3
  0,1                   0xA4

As suggested in   LTC2496 is generating zero as output data - Q&A - Precision ADCs - EngineerZone (analog.com). we have calculated the   2's complement of ADC raw data in order to retain actual value.

i.e 

if MSB=0

   Voltage=Raw data* LSB    i.e LSB=0.5 * Vref / 2^n

if MSB=1 

    data=Rawdata-2^n

    Voltage=data*LSB         i.e LSB=0.5 * Vref / 2^n

Can you please help us with the following issues

1.  When we started testing even through Vin is zero, we are getting voltages in the channels when it is configured as differential whereas when we checked both positive and negative channels separately as single ended channels, they we working as expected. what is the reason for this behavior?
2.  The information provided by @JCCillion in the above link regarding i didn't find it anywhere. can you please let us know how it is considered. 
3. Do we need any further calculation after actual raw data is obtained according to status flag? as it is mentioned in data sheet that "For differential input voltages greater than +FS, the conversion result is clamped to the value corresponding to +FS + 1LSB. For differential input voltages below –FS, the conversion result is clamped to the value –FS – 1LSB". if there is any further calculation required, can you please help us with the calculation.

Thanks,

Revathi